A year ago, I had totally fantastic pasta with shrimp and garlic at La Cueva del Pirata on Holbox, on the plaza. But you're probably looking for Mex/Yuc things...
In Kanasin, southeast of Merida just outside the ring road, there's a very famous place for abnormally large panuchos and salbutes--totally blanking on the name. Susana Internacional? Something like that. Everyone goes on Sundays--very festive.
Things on the Carib coast are coming to mind more easily, as I was just there last month. If you happen to drive through Felipe Carrillo Puerto, there are great panuchos at the bus station too. Gorgeous and cheap. Also, in the first town south of the turn to Mahahual, a Mormon family runs a little store and bakery--really good breads and cakes--they're just at the first speed bump.
Shrimp tacos at La Floresta on the highway in Playa del Carmen make a great road snack. I've also heard great things about a tiny shrimp taco stand at the entrance to Puerto Aventuras, but it was closed when I went (Sunday).
Everything in Campeche is delish--there's a really well known fish restaurant there, just north of the main plaza, and again I'm blanking on names. Champoton, on the gulf coast, has nothing but giant trucks and shrimp cocktail stands--definitely worth a stop.
And if you go to Cozumel, you _must_ eat at Sabores, a little resto a woman is running in her house--lunch only. So delicious and homey. On Av 5 between C 3 and C 5? Directly across the street from Las Anclas, anyway--which is a great hotel.
Tulum is busting out with places to eat: Italian is fantastic at Posada Margherita, Hechizo is a teeny-tiny place near the reserve--you have to email to book a table (google for info), and there's always Hola Prima, a little cabana on the old Maya plaza that serves...more panuchos and salbutes.
Scroll down for my post on Cancun...