As a developer for Kiva, and with some knowledge of Watsi's systems, I can probably answer this question, maybe I'll write a blog post about it actually, but the short of it is, the amount of effort involved for Watsi is going to be almost invariably greater than the reward gained from community contributions. (There's more to that but too much to fit into this format).
That said, take in to consideration that Watsi is quite likely using a bunch of the open-source software you are already familiar with. You can contribute to these projects, and thus indirectly be contributing to Watsi.
What I would like to see is non-profits sharing a list of the open-source software they are using (perhaps even weighted to what piece is most important to their operation) and thus giving eager developers such as yourself a roadmap towards helping them. (Bonus points for ability to reference specific bugs in said software, but that's somewhat rare).
