I'm talking to a non-for-profit about hosting and running their web site right now and they need a donations link on there page... I need a lead on a good online company to use for donations... I don't think PayPal is the optimum choice here.
You could try the amazon.com honor system, or look into 2checkout.
...aaand, Network for Good looks helpful. There's a link at the top of the site for non-profits.
See http://www.techsoup.org for nonprofit resources, including donation options.