I've always rather liked theme names for my animals. It helps keep them apart for me as well since I have so many!
For example, Dancing: Tango, Cha-cha, Samba, etc. Flowers: Daisy, Tansy, Buttercup, Orchid, etc. Any candy name: Skittles, Candy, Lollipop, Tootsie-roll, Jujube, etc. Nature: Sky, Cloud, Snow, Hail, Raindrop, Sunny, etc.
Other themes could be: Movie/TV Characters, Alcohol, Music, Magic/Mythology, Religious/Bible, Rocks/Gems, etc.
I also tend to name based on relation as well. Especially with my rabbits. For example, I'll name a daughter that I keep with the same first letter of her mother and any son I keep with the same first letter as his father. Siblings have the same first letter as well. I also keep detailed records, but it helps with day-to-day for me