I don't know if the same chef is still there, but we had the meal of a lifetime in a restored hacienda about 15 minutes outside Merida. It is called the Hacienda Xcanatun. We were stunned by the meal; when we were finished we thought about starting all over again and we were nearly in tears. It was the only time I've ever asked to meet a chef. Never had a meal come close to that, before or since. You can stay there, too, but it was beyond our budget. We heard that the breakfasts are fantastic, too. If I ever hit the lottery, first thing I will do is get on a plane, fly to Merida, and eat at the Xcanatun.
Wayan'e is one of the best taco places in Mérida. Some argue it's The Best. A bit out of the way if you're in Centro but definitely worth the taxi ride. Just get there early for the best selection.
And El Cangrejito in Centro. Excellent seafood (mostly) tacos, also a meaty, savory chicharrón option. It was definitely one of my favorites.
I was also a regular at La Chaya Maya in Centro and took visitors there to great success.
This was a couple of years ago.
The central market. Though with a warning: if you pick up a 1/2 kilo of kastacan, just cooked and hot, and eat it right out of the staining brown paper bag, you may very well be scarred for life. It'll haunt you. You'll search for it, but will never quite recapture it.
They say its better to have loved and lost than to have never loved at all.....