There's always Career Headquarters, the American Society of Association Executives career site (full disclosure: I work for ASAE). Career Headquarters leans more toward trade and professional associations than to philanthropic organizations, but there are some philanthropic organizations that advertise open positions there ... and if you set up a job alert, Career HQ will automatically send you an e-mail whenever a position fitting your criteria is advertised. You don't have to be an ASAE member to use Career HQ. www.careerhq.org
There's also Craigslist ... it's not a nonprofit-centric site, but the last two people I hired both found my ad on Craigslist, and they're both wonderful, so it's certainly worth a shot! www.craigslist.com
My organization is a member of the Center for Nonprofit Advancement (www.nonprofitadvancement.org) and they are a fantastic resource for all things related to the nonprofit sector - their Learning and Leadership Institute offers fantastic professional development courses that I've found incredibly useful and covers everything from reading financial documents, to fundraising, and (of course) board management. I believe they also have a job listing on their website as well.
I guess I'm a bit late to the party, but I run two sites/blogs that often feature non-profit jobs. I think you'll find them interesting, even if they're mostly geared towards college students.