Peg Leg Petes - This is a seafood joint on the beach that I much prefer over anything that Flounders can put out. If you hit a seafood joint on the beach I would recommend this over any of the others.
McGuire's Irish Pub - This by far one of the top 3 places to eat in Pensacola and if you can only make it to one restaurant while you're here, this needs to be the place you go. First of all they have a brewery inside of the restaurant and they brew great beers. Second of all I have eaten there more times than I can remember and have never ever had a bad meal there, the food is outstanding. If you arrive there to eat during the day time on a weekday there is a good chance the head brewer Mike Helf will be there and you can meet and chat with him, he normally does not work weekends or nights though.
Another seafood mention of mine is going to be Fish House down on S. Barracks St in Pensacola which is right on the bay, the seafood is outstanding the atmosphere is great.