What does having a project-specific nonprofit achieve that joining an existing organization doesn't?
I argue very little - as long as the organization you join uses modern financial systems, gives your project maximum autonomy, and is committed to providing you the services you need in an efficient, timely and transparent fashion.
At Sahana, we have a nonprofit that currently houses one open source software project and "research and action" program that implements our open source software and other technologies to solve real world problems.
Starting and maintaining any nonprofit organization is costly. Aside from getting the initial 501.c.3 status, you then have to build and maintain an active and official board with members who don't have conflicts of interest, file taxes, pay for insurance, maintain a few compliance that help secure contracts, occasionally work with a lawyer, move money, sign things, etc.
Maintaining that infrastructure takes dedicated administrative time/money. But once such a system is set up, the marginal cost of performing additional tasks of these types is very low.
That's why we're interested in bringing more open source projects into our organization. That way we can share the cost of administrative services, accounting, insurance, compliance, etc while also expanding our communities of technologists, developers and humanitarian professionals.
More about our organization and offer to ODK here: Concept Note A - Join an Existing Foundation - #10 by devinbalkind