Japan on a Budget

As mentioned before, here are the 3 main websites which I use when I plan/book for my own Japan trips.
- http://japan-guide.com/ (a comprehensive online guide to Japan)
- http://japanican.com/ (hotel bookings)
- http://www.hyperdia.com/en/ (train schedules/duration/prices)

However, if you are going for budget, here are some links which might be of help.

(Air Transportation)
Keep a lookout for promotional rates from the various airlines. I have ever gotten S$580 rate (inclusive tax & fuel surcharges) per pax for a return flight between Singapore and Osaka onboard Singapore Airlines. Once you get a good airline deal, then you start to plan your itinerary around it.
- http://singaporeair.com/ (Singapore Airlines)
- http://www.ana.co.jp (ANA Airlines)
- http://www.jal.com/ (JAL Airlines)
- http://www.delta.com/ (Delta Airlines: Singapore to Tokyo)
- http://www.jetstar.com/sg/en/home (Jetstar Budget Airlines: Singapore to Osaka Kansai)
- http://www.skymark.co.jp/en/ (Domestic flights: Skymark Airlines)
- http://www.flypeach.com/route/routemap.aspx (Peach Aviation)
- http://www.japan-guide.com/e/e2364.html (Guide to discount air tickets for domestic flights)

(Land Transportation)
Trains are usually more expensive than Bus. I would recommend the Japan Bus Pass instead of the JR Rail Pass. However there are also some really cheap Rail passes (JR Northern Kyushu Rail Pass is 1 example) so take a look around the various Passes there are out there before making any decisions.
For trains, there's many types of trains. There's Shinkansen (bullet train), Ltd Exp (skips many stations), Exp/Rapid (skips some stations), Local (stops at all stations). A Local train will be much cheaper (but takes a longer travelling time) than a Ltd Exp train. Shinkansen is the fastest and also the most expensive.
- http://www.limousinebus.co.jp/en/ (Airport limousine bus between Tokyo and Narita/Haneda Airports)
- http://willerexpress.com (Long distance Express buses)
- http://willerexpress.com/x/bus/dynamic/3/en/html/pc/buspass/ (Japan Bus Pass)
- http://www.nouhibus.co.jp/english/index.html (Takayama bus operator)
- http://www.alpico.co.jp/access/route_k/index_e.html (Nagano Bus operator)
- http://www.nishitetsu.co.jp/bus/highway/gb/ (Bus operator for Kyushu)
- http://transportation.fujikyu.co.jp/english/ (Bus operator for Fuji Five Lakes)
- - http://www.bus-hikaku.com/ (Bus Hikaku, cheap bus rates)
- http://www.jrbuskanto.co.jp/bus_route_e/ (JR Kanto Highway Bus)
- http://www.odakyu.jp/english/index.html (Odakyu)
- http://www.japan-guide.com/e/e2357.html (List of various Rail Passes)
- http://www.japan-guide.com/e/e2362.html (Seishun 18 Kippu Pass)
- http://www.japan-guide.com/e/e2361_05.html (JR Kyushu Rail Pass)
- http://www.japan-guide.com/e/e2361_03.html (JR West Rail Pass-Kansai Area)

(Food)
- There is a large variety of ready-packed food being sold at Japan's convenience stores (Lawson, 7-Eleven, Family Mart, Seicomart...etc) and they tastes quite nice.
- Usually, the basement of departmental stores are usually Food Halls, and when it's nearing closing time, many stalls will cut down the prices of their food, which is a good option to buy dinner during this time.

(Budget Hotels)
- http://www.toyoko-inn.com/eng/ (Toyoko Inn chain)
- http://www.superhoteljapan.com/en/ (Super Hotels chain)
- http://www.cubehotel.jp/en/ (Cube Hotel in Tokyo)
- http://www.solarehotels.com/english/chisun/ (Chisun Hotels chain)
- http://www.smile-hotels.com/english.php (Smile Hotels chain)
- http://www.theb-hotels.com/en/ (the b Hotels chain)
- http://www.tokyo-inn.co.jp/en/index.html (Tokyo Inn in Tokyo)
- http://www.sunroute.jp/ (Sunroute Hotels chain)
- http://www.hotespa.net/business/en/index.html (Dormy Inn chain)
- http://www.sakura-hotel.co.jp/ (Hostels in Tokyo)
- http://www.chuogroup.jp/selene/en/index.html (Hotel Chuo in Osaka)
- http://hotelkinki.com/en/ (Hotel Kinki in Osaka)
- http://j-hoppers.com/e_g_links.html (J-hopper's links to budget accommodations)

(Hostels/Capsule Inns) 
*most of these accommodations have only shared toilets/showers, so check before you book if you are particular about it.
- http://backpacker.ninja-x.jp/ (Directory of Guesthouse/Hostels for budget accommodation)
- http://www.key-yh.jp/index.html (Hostel chain)
- http://kshouse.jp/index_e.html (K's House hostel chain)
- http://www.khaosan-tokyo.com/en/index.html (Khaosan hostel chain)
- http://www.sakura-hotel.co.jp/ (Sakura hostel chain in Tokyo)
- http://www.jafplaza.com/index.html (Apartments and Guesthouse rental for long stay)

Hokkaido:
- http://inos-place.com/e/index.html (Hostel in Sapporo)
- http://khaosan-sapporo.com/ (Hostel at Sapporo)
- http://www.healingweb.net/nonaka/ (Guesthouse at Sapporo)
- http://www.youthhostel.or.jp/kokusai/ (Youth hostel at Sapporo)
- http://kuwataniya.com/ (Hostel at Otaru)
- http://www.tengu.co.jp/english/index.html (Guesthouses at Otaru)
- http://www.niseko-backpacker.com/index.htm (Backpackers Lodge at Niseko)
- http://www.annupuri-yh.com/index.html (Lodge at Niseko)
- http://www.bdlodge.com/ (Lodge at Niseko)
- http://hirafuhostel.com/ (Lodge at Niseko)
- http://www4.ocn.ne.jp/~furanoyh/ (Youth hostel in Furano)
- http://homepage1.nifty.com/TOIPIRKA/ (Lodge at Obihiro)
- http://www.masyuko.co.jp/ (Youth Hostel at Teshikaga)
- http://www.gogogenya.com/mokuzi.htm (Youth Hostel at Teshikaga)

Akita:
- http://www12.plala.or.jp/ohmagari-YH/index.html (Youth hostel at Akita)

Yamagata:
- http://www.ne.jp/asahi/pension/scrooge/eindex.html (Pension at Yamagata)

Iwate:
- http://www1.odn.ne.jp/tono-yh/index-e.htm (Youth hostel at Iwate)

Sendai:
- http://www.tojianguesthouse.com/sendai.htm (Guesthouse at Sendai)

Ibaraki:
- http://bptokiwa.web.fc2.com/ (Hostel at Ibaraki)

Nikko:
- http://www.nikko-suginamiki.com/ (Youth Hostel at Nikko)
- http://www.nikko-narusawa.com/ (Lodge at Nikko)
- http://www.turtle-nikko.com/turtle/ (Inn at Nikko)
- http://www3.ocn.ne.jp/~garrr/Rindou.html (Guesthouse at Nikko)

Chiba:
- http://www.backpackers-fuji.jp/ (Backpacker's hostel at Narita)

Tokyo:
- http://www.cheap-hostel-tokyo.com/ (Guesthouse in Tokyo)
- http://retrometrobackpackers.com/index.html (Backpackers Hostel in Asakusa Tokyo)
- http://bp-shinagawashuku.com/#home (Guesthouse in Shinagawa Tokyo)
- http://backpackersjapan.co.jp/english/ (Ryokan Hostel in Tokyo)
- http://www.first-cabin.jp/en/ (Compartment accommodation in Osaka, Kyoto, Haneda)
- http://www.sakura-hotel.co.jp/ (Hostels in Tokyo)
- http://www.kimiryokan.jp/index.php (Budget Ryokan in Tokyo)
- http://www.chiyoda-tokyo.com/english/ (Budget inn in Tokyo)
- http://www.hotelmaruchu.com/pc-e/index.html (Budget backpacker's hotel in Tokyo)
- http://www.palace-japan.com/english/index.html (Budget backpacker's hotel in Tokyo)
- http://www.newkoyo.com/index.html (Budget backpacker's hotel in Tokyo)
- http://www.aizuya-inn.com/ (Budget backpacker's hotel in Tokyo)
- http://kangaroohotel.jp/index.html (Budget backpacker's hotel in Tokyo)
- http://kshouse.jp/tokyo-e/ (Backpackers' Hostel in Tokyo)
- http://kshouse.jp/tokyo-oasis-e/index.html (Hostel in Tokyo)
- http://oakhostel.com/ (Hostel in Tokyo)
- http://www.khaosan-tokyo.com/en/world/ (Hostel in Asakusa, Tokyo)
- http://www.khaosan-tokyo.com/en/original/ (Hostel in Asakusa, Tokyo)
- http://www.khaosan-tokyo.com/en/ninja/ (Hostel near Bakurocho, Tokyo)
- http://www.khaosan-tokyo.com/en/samurai/access/index.html (Hostel in Asakusa, Tokyo)
- http://www.khaosan-tokyo.com/en/kabuki/access/index.html (Hostel in Asakusa, Tokyo)
- http://www.khaosan-tokyo.com/en/laboratory/access/index.html (Hostel in Asakusa, Tokyo)
- http://www.toukaisou.com/index.html (Backpacker's hotel in Asakusa)
- http://capsuleinn.com/shinjuku/en/ (Capsule hotel in Tokyo, only for Men)
- http://ace-inn.jp/index.php (Wooden capsule beds, Tokyo)
- http://www.tokyocozyhouse.com/index.html (Guesthouse in Tokyo, can stay for longer period)
- http://guesthouse1965.com/index_en.html (Guesthouse in Tokyo, can stay for longer period)
- http://www.tatami-guesthouse.com/ (Guesthouse in Tokyo, can stay for longer period)
- http://www.sakura-hotel.co.jp/ (Sakura hostel chain in Tokyo)
- http://www.housejp.com.tw/ (Budget accommodation at Ikebukuro)
- http://www.tatami-guesthouse.com/ (Guesthouse in Ikebukuro, stay for longer period)
- http://fiftys.com/en_index.html (Family Inn, somewhat near Disneyland/Disneysea)
- http://www.tokyo-inn.co.jp/ (Budget hotel at Magome, Tokyo)
- http://www.homeikan.com/ (Ryokan at Tokyo)
- http://www.sansuiso.net/ (Budget Ryokan at Tokyo)
- http://www.tamaryokan.com/ (Budget Ryokan at Tokyo)
- http://www.tokyo-guesthouse.com/index.html (Guesthouse at Tokyo, stay for longer period)

Yokohama:
- http://www.sakura-garden.org/ (Guesthouse at Yokohama)
- http://www.plaza-inn-shinyoko.jp/index_en.php (Budget hotel at Yokohama)

Kamakura:
- http://www1.kamakuranet.ne.jp/hase_yh/main_eng.htm (Youth Hostel in Kamakura)

Hakone:
- http://fujihakone.com/en/ (Guesthouse at Hakone)

Mt Fuji:
- http://kshouse.jp/fuji-e/index.html (Hostel at Kawaguchiko)

Shizuoka:
- http://kshouse.jp/ito-e/index.html (Ryokan hostel at Ito)
- http://www.izu.co.jp/~aoikaze/ (Youth Hostel at Ito)

Yamanashi:
- http://www.tim.hi-ho.ne.jp/innfuji/ (Inn at Yamanashi)

Niigata:
- http://nakatoshi.fuji.to/ (Lodge at Niigata)

Nagano:
- http://kshouse.jp/hakuba-e/index.html (Backpacker's Hostel at Hakuba)
- http://www.mthakubabackpackers.com/ (Backpackers' Hostel in Hakuba)
- http://hakubagondolalodge.com/ (Lodge at Hakuba)
- http://matsumotobp.com/en (Guesthouse at Matsumoto)
- http://www.avis.ne.jp/~miyasaka/index-e.html (Budget ryokan at Yudanaka)

Toyama:
- http://www1.coralnet.or.jp/buddha/etop/index.html (Budget ryokan at Takaoka)

Takayama:
- http://sakura-guesthouse.com/english/index.html (Hostel at Takayama)
- http://www.hidatakayama-guesthouse.com/sub1/B1.html (Ryokan hostel at Takayama)
- http://kyoto.j-hoppers.com/ (Hostels with branches at Kyoto, Osaka, Takayama, Hiroshima)
- http://kshouse.jp/takayama-e/index.html (Hostel at Takayama)
- http://www.d2.dion.ne.jp/~hidafyh/#飛騨古川ユースホステル (Youth Hostel at Hida Furukawa)
- http://www.irori-sosuke.com/ (Minshuku at Takayama)
- http://kuwataniya.com/ (Guesthouse at Takayama)

Nagoya:
- http://www.hostelann.com/Pages/english.aspx (Guesthouse in Nagoya)
- http://www.japan-net.ne.jp/~meiryu/english/nofrontpage.html (Budget ryokan at Nagoya)

Kanazawa:
- http://murataya-ryokan.com/eng/rooms.html (Budget ryokan at Kanazawa)

Ishikawa:
- http://nakatoshi.fuji.to/ (Youth hostel at Noto)

Shiga:
- http://shiga-an.com/index.html (Guesthouse in Otsu, Shiga)
- http://www.bscjapan.info/ (Hostel at Otsu)

Kyoto:
- http://k-guesthouse.jp/ (Ryokan Hostel near Kyoto station)
- http://www.kyotohostel.net/index.php (Hostel in Kyoto)
- http://www.kyoto-kinta.com/index.html (Ryokan Hostel in Kyoto)
- http://www.0757085177.com/english.html (Hostel in Kyoto)
- http://www.kazari-ya.com/index-e.html (Guesthouse in Kyoto)
- http://nashinokatachi.com/guesthouse-c.html/home.html (Guesthouse in Kyoto)
- http://kyoto-venten.com/index.html (Guesthouse in Kyoto)
- http://kyotoguesthouserenjishi.com/index.html (Guesthouse in Kyoto)
- http://kyoto-itoya.com/index.html (Guesthouse in Kyoto)
- http://kioto-kyoto.com/index_e.htm (Ryokan Hostel in Kyoto)
- http://www.koumekawa.jp/index.html (Ryokan in Kyoto)
- http://en.hostel-mundo.com/ (Ryokan hostel in Kyoto)
- http://kshouse.jp/kyoto-e/index.html (hostel in Kyoto)
- http://hannari-guesthouse-english.com/index.html (hostel in Kyoto)
- http://kyoto-chita.com/index.html (ryokan hostel in Kyoto)
- http://kyoto.cheapest-inn.com/index_e.html (hostel in Kyoto)
- http://kshouse.jp/kyoto-e/index.html (hostel in Kyoto)
- http://www.gojo-guest-house.com/ (Guesthouse in Kyoto)
- http://gh-project.com/index.html (Ryokan hostel in Kyoto)
- http://kyoto.hanahostel.com/ (Ryokan hosten in Kyoto)
- http://rakuza.gh-project.com/e/home.html (Ryokan Guesthouse in Gion Kyoto)
- http://www.first-cabin.jp/ (Compartment accommodation in Osaka, Kyoto, Haneda)
- http://www.bola-bola.jp/top_english.htm (Ryokan hostel in Kyoto)
- http://www.capsule-ryokan-kyoto.com/ (Capsule Ryokan Kyoto)
- http://9hours.jp/details/index/ (9hours Capsule hotel Kyoto)

- http://kyoto.j-hoppers.com/ (Hostels with branches at Kyoto, Osaka, Takayama, Hiroshima)

- http://www.khaosan-tokyo.com/en/kyoto/ (Hostel in Shijo Kawaramachi, Kyoto)

- http://www.khaosan-tokyo.com/en/theater/ (Hostel in Kawaramachi, Kyoto)
- http://www.bola-bola.jp/top_english.htm (Guesthouse at Kyoto)
- http://www.tojianguesthouse.com/kyoto.htm (Hostel at Kyoto)
- http://www.tojianguesthouse.com/sendai.htm (Budget ryokan at Kyoto)
- http://homepage3.nifty.com/yurakuso/index.html (Guesthouse at Kyoto, for longer period stay)
- http://www7a.biglobe.ne.jp/~greenpeace/ (Guesthouse at Kyoto, for longer period stay)
- http://www003.upp.so-net.ne.jp/rakucho-ryokan/ (Budget ryokan in Kyoto)
- http://www.gojo-guest-house.com/ (Ryokan hostel at Kyoto)
- http://www.hostelskyoto.com/annex%20e.html (Guesthouse at Kyoto)
- http://pascon.gozaru.jp/ (Guesthouse at Kyoto)
- http://unohouse.fte.jp/ (Guesthouse at Kyoto)
- http://www.ryokankyoraku.jp/ (Ryokan at Kyoto)
- http://www5.ocn.ne.jp/~seikis/index_e.html (Inn at Kyoto)
- http://www.ryokan-yamazaki.com/ (Ryokan at Kyoto)
- http://www.kohro.com/ (Ryokan at Kyoto)
- http://www.guesthouse-bon.com/ (Guesthouse at Kyoto)
- http://ton-bo.boo.jp/ (Guesthouse at Demachiyanagi, Kyoto)

(Amanohashidate)
- http://www5.nkansai.ne.jp/hotel/hasidateyh/eibunn.htm (Youth Hostel at Amanohashidate)

Osaka:
- http://u-en.hostelosaka.com/index_en.html (Guesthouse at Osaka)
- http://www.asahiplaza.co.jp/ (Capsule Inn at Osaka - available to both males & females)
- http://www.caminoro.com/ (Guesthouse in Osaka)
- http://www.guesthouseosaka.com/en/banana/index.html (Weekly/Monthly guesthouse in Osaka)
- http://www.first-cabin.jp/en/ (Compartment accommodation in Osaka, Kyoto, Haneda)
- http://www.caminoro.com/Facilities.html (Hostel in Osaka)
- http://www.bonsaiguesthouse.com/en/room.html (Guesthouse in Osaka)
- http://www.yamatoyahonten.co.jp/eng/room/ (Budget Ryokan in Osaka)
- http://www.hostel64.com/index.html (Budget Ryokan + Dormitory in Osaka)
- http://ten.hostelosaka.com/index_en.html (Hostel in Osaka)
- http://www.u-en.net/top/top_english.html (Japanese styled Hostel in Osaka)
- http://chuogroup.jp/en/ (Chuo Group, Osaka)
- http://www.chuogroup.jp/minami/raizan-english/main.html (Budget Hotel in Osaka)
- http://kyoto.j-hoppers.com/ (Hostels with branches at Kyoto, Osaka, Takayama, Hiroshima)
- http://hostel.oeh.jp/ (Hostel at Osaka)
- http://u-en.hostelosaka.com/ (Guesthouse at Osaka)
- http://www.hotel-taiyo.com/ (Backpacker's hotel at Osaka)
- http://www.hotel-toyo.jp/ (Backpacker's hotel at Osaka)

Nara:
- http://www.guesthouse-sakuraya.com/ (Guesthouse in Nara)
- http://www.ugaya.net/l (Guesthouse in Nara)
- http://yuzanguesthouse.com/ENGLISH/about-yuzanguesthouse-english.html (Guesthouse in Nara)
- http://homepage3.nifty.com/guesthouse-makura/index.html (Guesthouse in Nara)
- http://www.nara-backpackers.com/home.en.html (Ryokan Guesthouse in Nara)
- http://yuzanguesthouse.com/index.html (Ryokan Guesthouse in Nara)
- http://www5b.biglobe.ne.jp/~asuka-rd/ (Youth hostel at Nara)

Mie:
- http://www.hoshidekan.jp/ (Inn at Ise)

Wakayama:
- http://www.naxnet.or.jp/~yamagiwa/arida/ (Youth Hostel at Wakayama)
- http://www.bgh.jp/index.php (Guesthouse at Wakayama)

Kobe:
- http://kobe-kua-house.com/index.html (Capsule Hotel in Kobe -  available to both males & female )

Himeji:
- http://himeji588.com/ (Guesthouse at Himeji)

Okayama:
- http://www.kurashiki-sh.co.jp/ (Budget hotel at Kurashiki)

Hiroshima/Miyajima:
- http://www.backpackers-miyajima.com/index_e.html (Hostel at Miyajima-guchi)
- http://www.reinoinn.com/english/ (Budget inn at Hiroshima)
- http://kyoto.j-hoppers.com/ (Hostels with branches at Kyoto, Osaka, Takayama, Hiroshima)
- http://kshouse.jp/hiroshima-e/index.html (Backpackers' Hostel in Hiroshima)

Yamaguchi:
- http://www.e-yh.net/shimonoseki/indexe.html (Youth Hostel at Yamaguchi)
- http://www.paltopia.com/ (Budget hotel at Yamaguchi)

Shikoku:
- http://www.ecodogo.com/english/index.htm (Budget inn at Matsuyama, Shikoku)
- http://senguesthouse-matsuyama.com/ (Budget guesthouse in Matsuyama, Shikoku)
- http://www.matsuyama-yh.com/ (Youth Hostel at Matsuyama)
- http://www.hojosuigun.com/ (Inn at Matsuyama)

Kyushu:
- http://www.khaosan-fukuoka.com/ (Hostel at Fukuoka)
- http://www.kaine-g.com/ (Guesthouse at Fukuoka)
- http://www.kaine-g.com/english/e_index.html#setsubi (Guesthouse at Fukuoka)
- http://www.tabicolle.com/ENGLISH.html (Ryokan hostel in Fukuoka)
- http://www.khaosan-tokyo.com/en/beppu/ (Hostel at Beppu)
- http://www.happyneko.com/ (Guesthouse at Beppu)
- http://www.coara.or.jp/~hideharu/EngSmry.html (Budget ryokan at Beppu)
- http://www.nagasaki-hostel.com/index.html (Hostel at Nagasaki)
- http://www.n-kagamiya.com/en/guesthouse.html (Guesthouse in Nagasaki)
- http://nakashimaya.ikidane.com/eng.html (Ryokan hostel at Kumamoto)
- http://homepage2.nifty.com/minamiaso/guesthouse-english.html (Guesthouse at Kumamoto)
- http://www.aso-backpackers.com/index.html (Hostel at Aso Kumamoto)
- http://www.ks-kaikan.com/index_pc.cgi (Budget hotel at Kumamoto)
- http://nakashimaya.ikidane.com/ (Guesthouse at Kumamoto)
- http://www.green-guesthouse.com/english.html (Guesthouse at Kagoshima)
- http://www.cheaphotelasia.com/modules/tinyd0/index.php?id=29 (Guesthouse at Kagoshima)