On the Border (Mission Valley) there are 4 locations, but if they're all like this they rock.  Great food, decent prices, comfy seats, so-so service.

Ruby's Diner (Citadel Outlets) there was also one of these in Mission Valley, the food was good and the tables were nice (the booths suck).

Mimi's Cafe (Mission Valley) good food, comfy seats, good services. It was so good we ate their twice.