I spend a week in Gulf Shores every year visiting family that Snowbirds there, so I have a few 'local favorite' places in the area. My rankings are mostly based on the quality of raw shellfish served (love me some sea loogies), but they have other menu items....
Papa Rocco's - bills itself as "The home of warm beer and lousy pizza" and from the outside, the name seems like it fits. Pretty scruffy looking joint, but the oysters are the best in town (and huge) and the pizza is good (the shrimp or sundried tomato/artichoke pies are my personal favorites). Not fine dining by any stretch, but its a neat little local dive to check out.
http://www.paparocco.com/#2 on the list is the semi-famous FloraBama. Something along the lines of a beach shack / upscale biker bar - it looks like a stiff breeze will blow it down. Oysters are great, steamed shrimp are excellent, and the Po Boys are really good too. They host alot of local music, and it is a great place to just hang out and people watch.
http://www.florabama.com/And for sheer Tourist Trap epicness, give Lulu's a shot. Owned by Jimmy Buffett's sister, it is a monument to cheesy tourist eateries, but the live music is good and the food is decent. I've been there 3 times with the aforementioned family (who have yet to visit either of the other two places - I'm the only one in the family tree who enjoys raw shellfish) and eaten the mahi tacos and a bowl of seafood gumbo every time, and the quality of the dishes has been solid. It's unique to Gulf Shores, really cheesy and touristy, but a decent enough place. Long waits at prime dining times, so arrive early or late to avoid the clog.
http://www.lulusathomeport.com/index-live.phpThe Bon Secour Wildlife Refuge is a neat little place to go wander, especially if you have a camera. Not a huge place, but some decent trails with lots of wildlife hanging around. I usually spend a day there with a macro lens chasing bugs and stuff.
http://www.fws.gov/bonsecour/