Where to eat cheap in Japan ?

I have extended my plan from 21 to 27 days throughout the country. Any advice on where can I eat cheaply for lunch and dinner without self-catering or kitchen work ? I read about bentos from supermarket or Isetan basements but is there any proper place to eat on those take-aways ?
How to find or any tell-signs of any cheaper menu or restaurants ? Transportation and lodgings already took up a majority of my budget leaving me nothing much to eat :-)
Any tips on cheap places or restaurants to eat will be much appreciated.

Ramen shops are cheap, imo. So are most sushi places. You could stick to conbini bentos, if you'd like or onigiri. As for a cheap restaurant, though, Saizeriya comes to mind. Their foods are reasonably priced.

Gyodon is one of the cheapest options. You can eat a bowl of rice and meat for 500 yen or so. Ramen will cost you like 600~750 yen.

some supermarket have small corner with table/chair where you can sit down and eat the bentos you bought. some even have free green tea or water dispenser machine..

you can get bargain bentos 50% off 1/2 hour before closing time..u can buy those for ur dinner as well as your next day breakfast/lunch..

japan can be affordable if you know where to search..

Edward,

Since you say "Isetan" you're probably staying in Shinjuku, a place where locals won't buy their daily groceries. Needless to say, whatever country you go to, the closer you are to a city center the more expensive things are.

A great option is to aim for university towns. Universities itself always have a cafeteria where students and visitors can buy nutritious meals big and small in very reasonable prices. There are also reasonable diners and cafes around universities. If you are a student yourself, you might get lucky enough to get some discount at one of those places by showing your student ID.

A lot of people suggest conbini (convenience stores) but these stores are just "handy" and not always "cheap." At least it's better to go to supermarkets in the subburbs (again, not in city centers).

Lots of restaurants have menus with prices outside, or window displays of plastic food that look like the real thing, with prices, so you will know before hand how much it cost. in railways stations and around the stations there are always cheap food places.

have you seen this page:

http://www.japan-guide.com/e/e2028_food.html

Lots of good suggestions already.
I studied at Hosei university in Tokyo and never had to show my student id in the cafeteria so you could try there. The food is VERY cheap and of a fairly reasonable quality.
Chain stores (non US) will often have cheap options. E.g. Matsuya or Yoshinoya. Tachiguisoba (Standing noodle places) stands near stations are cheap and tasty. There are MANY MANY options for cheap food.

Gosh, I wonder why japan-guide.com doesn't tell you about university cafeterias on their "Budget Travel - Food" page :)

By the way, as suggested, most university cafeterias (not only in Japan, but around the world) have always been open to the public. You don't have to be a student at all to eat there.

The student ID I mentioned about in my previous post is about the other places outside university premises. Some diners have (Japanese) signs on the wall saying they give discounts for students. In that case, you might be asked for some kind of an ID.