Several years ago right here on Chowhound I met a poster by the name of Cristina who lived in Mexico. Over the years we've gotten to know each other and I've had the opportunity to visit her. This trip, complete with photos has been documented here - http://thediningdiva.typepad.com/
Dining in Guadalajara is heavily "see and be seen" so one of the nicest things about touring and dining with Cristina is that she knows where you can actually get really good food.
Even though I was staying with Cristina at her house, if you're checking into a hotel one of the first things you might want to do is check to see if the hotel has a copy of "Asi es Come en Jalisco", or Where to Eat in Jalisco. This is a little booklet, a Guia Gastronomica/Gastronomy Guide, put out by the Governor and Secretary of Tourism for the State of Jalisco, where Guadalajara is located. This little booklet is a pretty handly directory. It's broken down into sections of the city and contains a small (but not detailed) map of the area and pinpoints restaurants as well as other major points of interest. Intersperced throughout the booklet are recipes for regional specialties such as birria, posole, carne en su jugo and more. The booklet is in Spanish, but I think there is value to it even with limited Spanish skills, as it has a lot of photos, and, of course, addresses and phone numbers for close to 100 restaurants
Some of the places Cristina took me to eat include
Ma Come No and Italian restaurant and one of the very best restaurants in Guadalajara. I had a seafood risotto with some of the biggest, fattest, brinest mussels I've ever eaten. Pasta is house made, fish is cooked perfectly and there is an excellen salad bar, a rarity in Mexico. The tiramisu (not one of my favorite desserts) was outstanding.
Los Alteños Taqueria on Avenida Tepeyac in the Chapalita colonia, most taxi drivers should be able to find it. Tacos are $5 pesos each. (As of this posting, $5 is equal to about $.46 USD). The tacos are served from different stations at the back of the open air restaurant. You get in one line for al pastor, another for canitas, another for bistec or chorizo. One centeral flat top has big pieces of onion caremlizing away on it and you simply take the scoop and ladle whatever quantity of onions you want onto your plate. Salsas - verde, rojo, ranchera and avocado - are served in industrial containers from a stand in the center of the room. The al pastor is out of this world, the chorizo good but a little on the sweet side for my tastes. The carnitas are good, but pale in comparison to the al pastor.
In Tlaqupaque we ate at El Pescador Rojas. Once again a taxi driver in Tlaqupaque should know exactly where this place is. Here we ate wonderful chunky guacamole, shrimp empanadas with a crust that had been stained with achiote. Our entree were whole deep-fried huachinangos, which came with rice AND mashed potatoes, chayote and carrots al vapor (steamed) and a lettuce salad.
Other good options for Tlaquepaque would be Adobe a restaurant in a shop of the same name, or Casa Fuerte.
One of the specialities for which both Guadalajara and Jalisco are known is torta ahogada, or drowned torta. These are enormous torta sandwiches stuffed with pork and then cover - or drowned - in a thin chile sauce that has a pleasant kick, but will not singe off the taste buds. We ate tortas at La Torta Loca in the Mercado Libertad. The sauce is served on the side so that you can add as much or as little as you like. Whether you choose to eat at the Libertad or not - and it *is* packed with fondas of all strip and food safety - it shoudl be on the agenda for a visit. You can find almost anything under the sun there from bootlegged computer programs to hand tooled saddles to huitlacoche or a family offering knife sharpening services.
Not a food venue, but across the street from the Libertad is Las Cabañas, and old multipurpose colonial building. Inside, under the dome, are 54 murals painted by Jalisco native son Jose Clemente Orozco, one of the big 3 muralist (along with Rivera and Siquieros). They are totally worth a visit and extremely powerful in impact. English speaking guides may be available for the tour and if they are, do have them explain the meaning of the murals. Also Orozco played some perspective trickes with these murals that would be lost if you didn't know about the. Las Cabañas is so close to the market that you can do them both in the same day.
Though we didn't eat there, we did visit the fish market in Zapopan. There are several fish restaurants worth checking out. Same with the street vendors outside the Basilica de Zapopan on Sunday night. We did eat at the Tianguis del Sol, which is also in (where else) Zapopan. Great, huge, quesadillas made from masa and stuffeded with a variety of fillings. I am sure they were probably artery clogging fat bombs, but there is no getting around the fact that they were strikingly delicious - especially the cheese and rajas (strips of roasted chiles).
Of course there is Karne Garibaldi that institution of speedy service that serves only carne en su jugo, beef cooked in it's own juice until tender and succulent. You add the white onion, cilantro, lime and salt. Served with refried beans enriched with lard and corn kernels, tiny tortillas and rustic flame grilled knob onions. http://karnegaribaldi.com.mx
One of the trendiest spots in Guadalajara these days is Nude. I have been assure that clothing is not optional. http://nuderestaurant.com.mx/ Nude offeres transportation to and from hotels.
If you need a caffeine fix, there are 5 (and probably more on the way) Starbucks.
Guadalajara is a fabulous city. It's dynamic and has great energy.