We've taken our dogs to Baja for many years without any legal problems. The main thing to have is a current proof of rabies vaccination, and the only time we've been asked to show it was when returning to the U.S.. A health certificate from a vet will do the same thing, but the primary worry is rabies. For that matter, I have friends who have found dogs in Baja that they've fallen in love with and have taken them to a vet down there for their shots. No problems were encountered at the border with the paperwork provided from the vet.
Some things to remember are:
Take plenty of food for the trip as dog food in Baja is not cheap and quality food is hard to find.
We were on a trip where the outside temperature was about 95º, parked in the shade. I left the windows down a couple of inches and we were away for about an hour and a half. It had gotten to be 135º in the cab during that period. Our dogs were in an insulated Alaskan camper so they did not have any problems and, of course, we had left them plenty of water while we were away.
We always take along syrup of Ipecac (available at any drug store) in case they eat something that can be harmful to them (i.e., puffer fish - even dead ones, which are poisonous). Follow the directions on the bottle. The syrup will make them throw up; your dog will hate you for doing it, but will get over it. As gross as this may seem, it's better than a big vet bill!
An antibiotic cream (e.g., Neosporin) is good for hot spots or open sores. Also, we usually take along a general antibiotic in case they come down with an infection. Ask your vet, they will probably write you a prescription. The vets in Baja focus primarily on livestock and may not be up to date when it comes to pets.
If your pet happens to get sprayed by a skunk or decides to
roll on that dead seal over there
In Mexico, it's very common practice to put out rat poison to control populations of unwanted vermin, including dogs. I am not a veterinarian, but I have heard that the antidote for rat poisoning (WARFRIN is the actual compound) is vitamin K. Do not let your dog eat anything in Mexico, which is very hard to do. If your pet is peeing blood it is possibly due to rat poison, and you are in trouble. If you can bring intravenous vitamin K, then you are ahead of the game. They pee blood because the warfrin destroys the liver.
Strychnine is also a common poison in Mexico. Same thing, they put out bait for vermin with the strychnine in it. People need to keep their dogs in control at all time, and be conscious of any damage they do to Mexican property, I have heard stories of local Mexican farmers getting mad at gringo's and poisoning their dogs to get rid of "the problem."
If this is a real worry for you, one idea would be to place one of those muzzles on your dog, puppies and young dogs especially, while in and around populated areas. That would help keep them from eating anything you wouldn't want them to.
Other things to remember:
This isn't necessarily everything