Here are two brief but useful blogposts - with photos:
Grocery Shopping in Japan @ Irrational Exuberance
Reliable Mealtime Friends @ Irrational Exuberance
Also, check out
Bento.com
Often the economics of cooking for one mean it's less expensive to just eat out or get takeaway.
Two readily available fruits sold 'reasonably' at most grocery stores are bananas and mikans.
Hanamasa is a chain of wholesale foods stores that are often open 24 hours.
Another 24 hour store worth keeping an eye out for is
LAWSON 100:
Most items are priced at Y100 and they include groceries including fruits, vegetables and convenience foods; pretty good for student who is on their own...