Pros
A flexible work environment with a great mission. Outstanding people to work with (this wasn't always true, but all the terrible people are gone now). So if you're looking for meaningful software development work, this is a fantastic place to be. There's always plenty of work to do, and we try very hard to tailor the work to people's strengths or interests. We've gone through several rounds of changes in the past year to try to get past the difficulties that we used to have, and it's so much better than it was even one year ago.
Cons
You're only going to be able to go so far "up", so if you're in an early-to-mid part of your career, this may only be a 2-4 year job for you. The development isn't greenfield, because we have existing systems that we have to work in; it's definitely geared towards people who are interested in the challenges of maintaining and improving existing software. Also, we are a non-profit, so the pay isn't going to be as good as at successful for-profits or soon-to-be-gone startups. The worst problem, and this is one you can potentially help with, is that our diversity went way down during the rough times. We definitely don't want a monoculture, so I'm hoping we can reverse this trend soon.