Mel's Diner on Mission Street @ 4th Street (a few yards from the Moscone Center) is inexpensive and spotlessly clean. I eat there frequently.

Little Henry's family run Italian restaurant at 955 Larkin Street @ Post Street is another favourite. The decor may be somewhat Spartan, but the home-made food at very reasonable prices is well worth the visit. Very friendly manager (he even remembered the meal I had eaten three months before).