Hey, spent a week in Belize last month, and thought I'd post a short report here before I forget.
We spent half the time on Caye Caulker, and half the time on Ambergris, mostly in San Pedro.
In Caye Caulker, the roadside BBQ is a great deal, and worth having. We ate at Rose's BBQ a few times, right up the street from Habanero's. They have chicken and shrimp, and will often have fresh caught fish like grouper, barracuda, and so on - always worth asking.
Of the more traditional restaurants, we ate at, in order of quality, Habanero's, Agave, and Don Corleone.
Habanero's was probably the best meal we had on the island - the food was good but not exceptional. Had a coconut crusted snapper that was quite good. We ate at Agave, which again was good but not exceptional. They absolutely have the best rum punch we had on Caye Caulker, however, and some of their specials were good. I'm listing Don Corleone third - it definitely was not bad, just not memorable, which is not surprising for an Italian restaurant in that part of the world. The food was forgettable, but it was fun to eat in that type of restaurant, such a contrast to the primary culture in the area, and they had a nice little wine list.
That pretty much covers it for Caye Caulker. For me, the best bet was a fresh piece of grilled fish with rice and beans and some vegetables. The 'nicer' restaurants are ok but nothing exceptional. There are a few restaurants built out over the water, great spot but the food was not great. If they'll let you, order a couple of drinks and bring out some roadside bbq - great view and great food!
Ambergris Caye, and particularly San Pedro, offers many more options. The best meal we had was at Capricorn, which is north of San Pedro and requires a water taxi if you are staying in San Pedro. However - absolutely worth going to. A beautiful setting right on the beach, and the grouper special, as someone else mentioned, is a must-have.
Also, Wild Mangoes in San Pedro is excellent. On the beach, and their banana/chocolate/ice cream/tortilla dessert is fantastic.
Other small, local places in San Pedro that we really enjoyed -- DandE frozen custard - great dessert. The Reef - popular with locals, and great for lunch. Also, not exactly a food recommendation, but for a different experience, rent a golf cart and drive north over the bridge to the Beach'n'Kitchen - there's a bar here built over a pier - great view and a completely different experience.
Had a great time in Belize, and some good food - glad to provide more details! Have a great trip if you go.