I've tried just about all the sheep related programs you can download My favorite right now is flockfiler. You can use the evaluation mode indefinitely if you don't mind a little popup coming on every once in a while asking if you want to register. It doesn't bother me enough to pay $50 to register it.
I like that I can modify its categories to track things like FAMACHA scores or number of horns. It's easy to add notes for individuals or whole groups if just one gets sick or you are vaccinating your whole flock and adding new lambs or bought sheep wasn't a problem at all. It even archives things like weight and wool production so you can compare individuals to your flock average to make breeding decisions easier.
I also have tried breeder's assistant which had a pretty steep learning curve and I didn't like it very much and ranch manager which doesn't have a long term free option but works well and is easy to use. I can't think of any of the others right now but I spent a week last summer going through all the ones I could find to pick one that would work best for my flock.