Degei is still my favorite. It's had some bugs in the past, but support is good, and the latest version seems fine.
It does pretty much everything--track feed, shed, poop, notes, pictures, breeding, clutch labels, generate clutches (when they hatch), genealogy, cage card printouts, record printouts, tracks feeders and feeder costs, etc. My favorite is something surprisingly few of the newer programs seem to handle, which is giving you a printout sheet of everyone who's due for a feeding according the schedule you set up for them, and when they last ate. It's user-friendly, and setup is not horrible. (I hated trying to set up Metzcal, for example, and gave up on that after a short time).

I also use iHerp, for the lineage database, and so customers can have a nifty record with all the photos if they want it. (I also like having backup records there). iHerp has a ways to go to make it convenient for tracking collections beyond a few animals, though.