There's the old stand by of doing them by hand.
Do you know what a pain that is? and reading the writing of some folks is a bit of a challenge!
There are free ones : sit/stay has one. Each pedigree has to be manually entered but you can email it to yourself. Useful only if you have a few rabbits that you need pedigrees for OR are waiting to get a paid system and don't want to handwrite out a litter as you can print off more than one copy of a given pedigree.
and there are ones that you can purchase
Kintraks is what I use. LOVE this program. It's affordable. Does what I want it to. The owner is quick to respond. It changes and grows. ONE program handles all my livestock needs. I have it for rabbits and guinea pigs and if I wanted to add cattle, sheep, goats, spiders and what have you I could do that! All for one measly $20! It has on-line storage and such like as well.
Global Pedigree. This is a new program to me. I haven't really looked at it a whole lot.
Breeders's assistant. Tried it, was unimpressed. Removed it from the computer since it was a pain to work with. I know other breeders love it though so.. depends on your needs. It may have changed in the last four years though.
Evans. This one is highly popular among the rabbit folk. Too pricey for my blood though. A lot of people swear by it though. Has a genetics component for extra dollars as well.
Cunitec. I actually have this on my computer. I can't recall what my thoughts were on it. I just love kintraks though so I haven't really needed to use it. :)
Homestead Apps Homestead Apps released an app to help hobby and urban farmers manage their animals - My Animal Manager. Here is a post that talks about this program as I've never seen/heard of it before.
So am I missing any? If so let me know please.
Okay are some that I found that I know nothing about
the breeders program. seems oriented to cats. dogs. horses.
various genealogy apps work as well. :)