We use ShelterLuv, which has been great for helping us stay organized with medical information, intake address, and which trapper was involved. Plus they charge you per *adopted* animal. There's no charge for animals with a different outcome (TNR'ed, transferred to another shelter, etc)! We're primarily TNR, so it's very affordable for us. We are in Milwaukee, WI ( ~600,000 people).
Downside is that it doesn't have an option to map out colonies or something like that (we have that recorded separately on Google Maps, also with locations for our volunteers).