(holy crap the planets must be aligning...Lumbollo and I are on the same page!!!)
Open Kitchen (http://www.theopenkitchen.net/ - broken link) is probably the most "whole in the wall" type of place I've ever been too...and it's not bad food either! Yes, they're still open. They're a Greek-Italian place (like many are) and offer a sweet tomato sauce (I say that because some prefer a traditional savory sauce, calling sweet fake). Lots of history and friendly staff.
I don't particularly have a favorite spot in town, but I do have regular places:
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DaVinci's in the University City/Davis Lakes area...NY style pizza, good and decent prices
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Villa Francesca in Uptown at the corner of 7th and Caldwell..."Grandma's Special" pizza is one of the best unique pizzas I've ever had