I'm starting a small non-profit, that accepts donations from "members" in the form of monthly dues. I'm wondering if there are any web apps out there that will help me track their payments? Something easier than keeping a spreadsheet in excel. Integration with paypal to automatically update the data if they pay online would be nice, but it also needs to support manual entry, as some will pay via cash / check.
I don't know of any publicly available web apps that meet your specs but (provided that you have a web host), there's a script that sounds close to what you need called the "Paypal Membership Subscription Manager" on www.codecanyon.net for $22.
According to the developer description, it has the following features: