The model for my fundraising site is that 100% of the money that is raised on each project goes to the project owner (minus Paypal fees). I plan to make money off donations directly to my site, and sponsorships and premium options.
Ideally I'd love to have an option so that when someone donates to a project, they can optionally choose to designate additional funds towards my site itself. So they'd sign up to give $25 to a certain project, and then click a radio button to donate an addition $5, $10, $100, etc. towards my site. It would need to keep track of those funds separately from the project.