Don't drink the tap water. In general, avoid drinking tap water throughout Central America, unless you hear otherwise regarding a specific hotel or island. There are numerous waterborne pathogens that can lead to an upset stomach or worse if ingested. Fortunately, purified water is readily available.
Watch out for ice. In the same vein, avoid ice in Central America unless you know it's made from purified water. (Many places do use purified ice – just ask!)
Boil it, cook it, peel it or forget it. Central America boasts an incredible variety of fruits and vegetables, and indulging is irresistible, especially in the former. However, eating unpeeled fruit or fruits/vegetables washed in tap water can make you ill, potentially in serious ways. That's where the easy-to-remember catchphrase comes in: "boil it, cook it, peel it or forget it." If you can't cook it or peel it, don't eat it.
Be wary of street cart food. I won't suggest avoiding street carts entirely, unless you have a very sensitive stomach. Some of my favorite Central America meals have been from street carts. However, street cart fare is definitely a gamble, in both quality and cleanliness. If meat looks like it's been sitting out a long time, probably not the best idea.
Watch out for stray dogs and cats. I am a diehard animal lover, and the stray dogs and cats in Central America are both heartbreaking and unavoidable. But petting them is another story. A dog or cat bite is serious business, especially if you're traveling in a rural area where medical attention is harder to find. What's worse, rabies is alive and well in Central America, and nothing wrecks a vacation quicker than a deadly disease.
Don't feed the wildlife. Human food can make wild animals dangerously sick.
Don't pet the wildlife. I know that sloth's super-slow getaway makes him an easy cuddle target. But don't. First, because animal bites not only hurt, but can also spread illness. Second, because it's not good for the wildlife. If you'll be volunteering with wildlife, getting a rabies vaccine is usually recommended.
Bug spray is your best friend. Okay, not really, but it's very important. Mosquitos afflict all of Central America and range from a minor nuisance to a major annoyance, depending on the region and the season. Besides causing itchy bites, the little bloodsuckers spread diseases like malaria and dengue fever (which has no vaccination). Your best defense is long sleeves and pants in the evenings – which can be tough, I know, in steamy jungle places – treating certain articles of clothing in permethrin insect repellent, and spraying exposed skin with DEET insect repellent (at least 25% DEET, but not over 50%). I hate using bug spray, but it's only for a limited time, and I think I'd hate dengue more.
Get your vaccinations! A few weeks before you travel to Central America, check the CDC and see what vaccinations are recommended for every region you're traveling in. You'll always want basic boosters like tetanus, but in certain rural or forested areas, the CDC recommends vaccinations like Hepatitis A and B, Typhoid and Yellow Fever (all vaccines I've gotten). If you'll be working with animals, the CDC usually recommends a rabies vaccine. In addition, many Central America regions are malarial, and malaria pills are recommended.
It's also smart to ask for a prescription for Cipro or another heavy-duty antibiotic, in case of serious stomach illness. Many medications that are prescription-only in the United States can be bought over-the-counter at Central America pharmacies. The hardest part is describing your problem in Spanish!