As I have many guests coming and the blogs have become congested with restaurants that have bitten the dust I will just list here some places you might enjoy. I eat almost exclusively at home. Last year my chickens convinced me to stop eating chickens and this year my yoga convinced me to stop eating meat and I suspect if I go anywhere near the sea or an aquarium I'll stop eating fish as well.
You'll find the addresses for the places I mention in my blog or from Mr. Google.
I go to Marlin Azul very often and Cangrejito sometimes. Both are good and inexpensive options for lunch in centro. I go to Miyabi when I want fish but a tourist doesn't crave Japanese in Mexico and you should go to Mulle Ocho or La Pigua for lunch or dinner and ignore the decor and atmosphere of both. El Pez Gordo has several locations but the one in centro closed this fall. They had decent baja style tacos.
For something special (and I mean that literally and cynically) try Hacienda Xcanatun's Casa de Piedra or Rosas y Xocolate or the newly reopened Nectar. I hear good things this year about all of these places. When I want a special meal I get on a plane to New York or Paris. I don't do special in Merida but you might not have a choice. If you're out of your mind you can go to this years Newest and Most Special place Ku'uk which is spectacular molecular smoking spinning and bell ringing with never ending tasting menu's.... UPDATE: Jan. 9, 2013 had dinner last night at Rosas y Xocolate and it was very good...still I'd order with caution...
La Rueda is the local steak house where the locals have long lunches in front of televisions and an astroturf playground but don't let that scare you. LaRecova has survived the popular crowd and has settled down into a pleasant place to dine I hear. The ""trendies" sent me running 3 years ago. Trotters is where everyone goes (except me). None of those are in centro so in centro if you want a steak go to Pancho's which is owned by Trotters. Update September 2013 Trotters has opened a new location of El Tratto in Santa Lucia park.
Casa San Angel has a good breakfast and lunch menu and is a pleasant place to hang out for coffee and dessert. The newest hotel is Mansion Merida on the Park and I gave this place a walkthrough but could not give it a sit down and neither should you. Rosas y Xocolate is a place you might want to try the bar on the roof terrace or the informal dining room in the courtyard before plunging into the Dining Room Xperience. Casa Balam is very very old school but safe for grandma and private bankers.
Chaya Maya is a place you're going to go but I can't...The new La Chaya is even worse albeit prettier. La Reina de Itzlana is a market stall with good food after 8pm in Santiago. La Tradicion has a new central location on calle 60 and also safe for granny as is the Los Alemendros in the Fiesta American Hotel or Mejorada park. I'd just go to the market and eat if I were you and if that scares you then drive out to Hacienda Teya or go to Mani and to El Principe de Tutul Xui which is what I would do.
All of the Mexican cooks have moved to America or Europe except Ana Sabrina who makes tacos in Santa Lucia park on Sunday til 2pm. La Reforma has good Mole and Chile Rellenos and I suppose Frida's does too. Those are the places to have Chiles en Nogades this season. Pancho's is the most TexMex option if you like that cruise ship atmosphere with load music and costumed waiters. My first choice is Apoala a Oaxacan restaurant that just opened this fall in Santa Lucia park.
There are some decent Italian places opened by real live Italians in Centro you're only options are Rafaellos Pizza and Oliva which just opened in November 2013.
I would recommend that you really try the food of the local women who cook in their homes mostly and offer a table or three and take out. These are called cocina economica and you can take your Tupperwear there at lunch time and walk away with the special of the day. I wouldn't be afraid to eat in the market stalls if you see others doing it. I've been sick once from food in 12years. The odds are in your favor.
** my gold plated rule is if you have a doubt then order appetizers to start and then if they are good order something else. If it's bad get the check and go somewhere else. Life is too short to eat shitty food.
Happy New Baktun and Happy New Year