Check out Travelocity, I've seen some pretty good deals on there.

I live in Japan and I can tell you that Japan is a very expensive place to travel. But a good way to save money is a JR pass-- get one. they cost like $250 for a 7 day pass and upwards for longer visits, but trust me, it's a very good deal. You get unlimited use of the Shinkansen(bullet train).

For lodging, you can stay in a business hotel for about $50-60 US a night. In bigger cities there might be youth hostels, but everywhere there are Ryokan, which are Japanese-style mom-n-pop style places, they're really cheap but you have to share a bathroom. And no trip to Japan would be complete without a night in a capsule hotel. Go to an onsen(hot spring bath), that is a huge part of Japanese culture.

For food you could can eat really cheap stuff like ramen, soba and udon for like $3-5 a meal. A cheap healthy snack available in convenience stores is called "onigiri", a rice ball wrapped in seaweed, usually with like tuna or salmon inside. If you're a vegetarian, good luck. Every place in Japan has some kind of food that it's famous for and you should try it.

If possible, try to see some kind of cultural festival somewhere. Japanese people are normally a little shy and reserved, but they let their hair down at the festivals. You'll have tons of people taking pictures with you, plying you with alcohol and trying out their English on you.

The Lonely Planet Japan is a pretty good source and I'm not telling you anything you won't find in there, but if you have any questions feel free to email me.

use hotwired.com

it lets you choose mutilple airport (starting) and ending points to save you the most money. It's the best I've seen so far and beats out some of the internal pricing i get directly from the airlines.

Own sick reasons? You'd be better off going during high school summer vacation. That's when all the schoolgirls from all over the country flock to tokyo to make money from "compensated dating". In the summer, you'll get a good "bang" for your buck because of the said flood of amateurs.

sorry in advance for any typos. i am too lazy and busy to really give a damn...

the JR pass is a good idea, for certain - especially if you want to trvael all around japan. make sure to go from north to south, so you can really see everything it has to offer. the onsen in northern japan are the best. tokyo is just cool (where i live). and hitting up kyoto and fukuoka is also pretty cool. you can see a LOT of cool cultural things about japan in kyoto, and fukuoka is so far south that you won't run into as many other gaijin, and as such will be treated a lot more differently. (every time i go to fukuoka, i get a lot more people coming up and talking to me than when i go around tokyo.)

for japan lodging on a budget, the ryokan are really a good idea, but your japanese speaking abilities may have ot be on the decent side - once you get outside of central tokyo. but in all honesty i would go with the business hotels, as you've got a much better chance of people there speaking some english.

for japan food on a budget, unless you plan on only eating noodles and simple rice dishes like gyudon everyday, expect to spend a lot of money. you can, however, go to one of the 8 billion convenience stores open 24 hours a day and get cheap bento, which they will microwave for you there for free. (besides... no trip to japan is complete without trying to eat spaghetti with ohashi - aka chopsticks.) there are macdonald's, wendy's, and KFC's all around larger cities, as well as the japanese "fast food" chains, like matsuya, yoshinoya, pepper lunch, mos burger, etc.

make sure to hit up shinjuku or akihabara when you visit tokyo. shinjuku is the most travelled train station in the world - something like 2 million people go through it every day - and that area of tokyo has all kinds of cool shops. akihabara may have a few more electronics shops than shinjuku, and way more otaku things, but it also kind of stinks. (being an otaku in japan is not a good thing, apparently because many of them do not know how to bathe. ^_^)

the best thing for you to do to arrange transportation or lodging is to see if any friends of yours live here, and can guide you to places to find good deals, etc. my wife - native japanese - does all that searching for us when we want to travel around, and her father owns many hotels throughout parts of japan, so we have a bit of an unfair advantage when we want to go and stay somewhere outside of tokyo... but i managed to spend three weeks out here before i met my wife and spent less than 3k for everything, including all the goodies i bought for myself and others, and i travelled very far throughout the country. (the 3k did not include my plane tickets to and from japan, though - just so you know. that ran me just under $700 for my round trip ticket because i went durng an off season, and i got my tickets a few months in advance.)

good luck, and unless you keep your eyes closed and your ears covered the whole time you are here, you will have a great time. (but then again, i am sure there are some love hotels which specialise in the whole sensory deprevation for everything except your... well... you get the idea.)

and in response to drew's post... unless you're rock ugly, and have no sense of "coolness" about you, you shouldn't have to pay for that sort of thing.