I find that the ones from AQ40 and Naxxramas go for the most money, but it highly depends on your economy. Just this morning I made 3800G from the Viscidus Globule. Prices of pets can easily be doubled if you have the time and effort to level them to 25, but I don't.
That about covers it, got any questions, just ask.
NOTE: To sell the pets you must first learn them, find them in your pet journal, right click them, then put them in a cage.
PLUS in 5.3 three old TBC raids will be dropping rare battle pets as well, that means more money!