It's quite possible to eat decently in Japan and save money at the same time. A lot of people think food is ZOMG teh expensav in Japan, but just like shopping for everything else, you just gotta go where the deals are and partake in the expensive stuff only in moderation.
For breakfasts, you can get oatmeal or cold cereals with milk. However, breakfast cereals aren't that popular in Japan, so you'll have a limited selection to choose from. However, the store I shopped at ("Nafuko" in katakana; sorry, not sure how to input Japanese on this computer) had big bags of granola for, like, 400 yen, so I'd often buy that and have it for breakfast. Sausage is decently priced; eggs are a bit expensive, but affordable. Pancake mix is cheap, and fruit jams can be cheap-ish; use those instead of syrup. Butter is expensive.
For snacks, convenience stores will be laden with potato and sometimes corn chips, as well as a large assortment of candy. For something healthier, get an onigiri (rice ball) which will usually run you about 120 yen, depending on the filling. My favorite was "okaka" (in hiragana); bonito fish. I usually hate fish, but that stuff was awesome. Most of the other ones will have names in kanji, though, so sometimes you'll have to play a game foreigners in Japan refer to as "onigiri roulette." Be careful with "shi chikin" (katakana); amusingly, it's actually tuna... Chicken of the Sea. Ice cream as we know it (sold in boxes or buckets) is impossible to find, but you can find it sold in single-serving cups, or as ice cream bars or other treats.
For dinner, pastas are cheap and tomato sauces are affordable; add in some hamburger or sausage and bam, ya got spaghetti. Sure, rice is cheap, but it tended to take a bit too long to cook for my tastes (pun intended). For roughage, potatoes are cheap and lettuce, tomatoes and carrots are affordable. Nafuko had an area of the store where older veggies were sold at a discount; I often raided that little table like a Hun.
Fruits-wise, bananas and "mikan" in katakana (tangerines, I think) are cheap; I ate a lot of those. Pineapples, apples and oranges are occasionally affordable. Forget about having any kind of melon. Fruit juices (jyusu, kata) are affordable; I drank gallons of one that was a mix of orange and "mikan" juice (unfortunately the name escapes me at the moment) that was friggin' delicious.
For beverages, besides the aforementioned juices, there's also plenty of green tea; my favorite brand was "hajime (hira) ichi (kanji)." There's plenty of Coke; Pepsi is a bit harder to find. Lemon-flavored sodas are popular. You'll never find a root beer. Sports drinks like Gatorade and Pocari Sweat (both romaji) are common. (Pocari Sweat tastes a lot like its namesake, by the way... barf.) Milk is expensive, and forget about finding low-fat or non-fat milk. You'll have a hard time finding a vending machine that doesn't sell both hot and cold canned coffee (ko-hi-, kata, though usually coffee cans will have plenty of English on them), and sometimes cocoa (kokoa, kata -- note the non-silent "a").
Sorry for the late reply, OP, but I don't visit this board very often.