The phrase "guinea pig" entered the language a long time ago as slang for "test animal", but I've yet to make a compound that's crossed a guinea pig's lips. Guinea pigs are still used for a few special applications, but since the beginning of my career, I've been surrounded (metaphorically!) by rats and mice.
Of the two, I prefer the mice. That's probably because they're smaller, and need correspondingly less effort from people like me to make enough drugs to dose them. The animal-handling folks prefer them for similar reasons: rats are more ornery, and they can fetch you a pretty useful bite if they're in the mood. When I was working in Alzheimer's disease, we had a small group of elderly rats that we were checking for memory problems. If that makes you think of rat-sized rocking chairs, think again. These were big ugly customers, feisty, wily critters that knew all the tricks and were no fun to deal with. Give me mice any day.
Of course, there are mice and there are mice. "Wild-type" mice are pretty hearty, but we don't use rodents captured out in the meadow. They're too variable, not to mention being loaded down with all sorts of interesting diseases. Every rodent we use in the drug industry comes from one of the big supply houses. Even our wild-types are a particular strain, identified with a catchy moniker like "K57 Black Swiss."
You're in good shape if you can use regular animals for your drug efficacy tests, but we often work on diseases which have no good rodent equivalents. People in diabetes projects, for example, often use mutant mice such as the db/db and ob/ob strains, which are genetically predisposed to put on weight. Eventually they can show some (but not all) of the signs of Type II diabetes. They can get pretty hefty - you'd better plan on making more compound if you're going to be testing things in those guys. Meanwhile, cancer researchers go through huge number of the so-called nude mice, a nearly hairless mutant variety with a compromised immune system. You've got to know what you're doing when you have a big group of those guys, because you can imagine how a contagious rodent disease could tear through them.
All the mutant animal lines are damaged in one form or another, since they're supposed to serve as a model of a disease. (Actually, most mutants in any animal population are damaged, since in a living system it's a lot easier to make a random change for the worse than it is to make one for the better.) They're just not as robust as the wild types. They need special handling, and they can't tolerate all the methods of compound dosing that a normal animal can. In some cases, you're restricted to the mildest, tamest vehicle solutions. (You know, the ones you can't get any of your compounds to go into.)
And there's always that nagging doubt about how valid your animal models might be. Some research areas have worked out a pretty good correlation between what works in people and what works in mice, but many of us are still stumbling around. The more innovative your work, the less of an idea you have about whether you're wasting your time. 'Twas ever thus.