Emerald Bay and Seascape are the only places in Destin proper where you can get a round for much less than $100 without twilight/discounts/etc. That said, go on golfnow.com and you should be able to play basically anywhere for <$100 if you play later in the day (it will be hot as balls, though).
For a real bargain on golf, you're gonna have to drive a ways. Even the lower tiered places in Destin are pretty overpriced during tourist season, IMO.
Depending on where you are staying, there are places relatively close to play on the cheap. Niceville (just across the mid-bay bridge north of Destin) has Bluewater Bay CC. It's decent but very short and tight, so not the type of course I enjoy (you could basically leave your driver at home). Eglin AFB has two courses in Niceville that are open to the public. I think these are pretty cool because they are different from most area courses since they have a good bit of elevation as opposed to the basically flat courses nearer to the water. Falcon is my favorite, but Eagle is the easier of the two. Rocky Bayou CC is a nice little drag too, and open to the public.
I always tell people the absolute best bargain in the area is Blackstone in Mossy Head (about 45 min north of Destin). You can play for like $30 with a cart, and it is a really good, fun layout. Almost never crowded.
To the west, Fort Walton has two 18 hole courses at the muni. They're both pretty easy courses (good confidence boosters), and I'm always amazed by how decent they're able to keep it with all the duffer traffic that they get. Shalimar Pointe has a really cool layout, but the new ownership has let the course go way, way downhill. Wouldn't recommend it unless you get a great deal and are really just looking to play cheap.
Further west nearing Pensacola, you have Hidden Creek and Tiger Point in Navarre/Gulf Breeze area, and they're both decent but I wouldn't drive this far unless you just got a screamin' hot deal.
If you really didn't mind driving and just wanted the best golf for the money, you could go 1.5 hrs west to Mobile and play Magnolia Grove on the Robert Trent Jones Golf Trail. Outstanding course and can be played for <$50 later in the day.