Definitely go to the New Yorker Deli out where Cervantes meets Scenic Highway. Tre Fratelli is an excellent Eye-talian joint. I'm a big fan of Bagelheads (up the street from McGuire's) - best breakfast in town, if you're a coffee-and-bagels kind of guy. Can't beat Hub's for sandwiches. McGuire's, obviously, if you go during slow(er) hours (avoid from Friday afternoon to Sunday night). Jerry's kicks absolute ass for Cajun. I really like Lillian's Pizza out on Perdido; the service kind of sucks, but the pies are excellent and the waitresses are pretty hot.
Further afield, Fudpucker's in FWB and Destin (not Fudruckers, altogether different) has great seafood and burgers. I don't know if The Boathouse in Valparaiso (outside Eglin) is still open, but it was also good.