We're currently developing more than one Force.com-based application for delivery through the AppExchange.  We're using the Force.com Migration Toolkit and the Force.com IDE plugin to move metadata back and forth between dev orgs (as well as test, integration, etc., stages) and our SCM tool.  Each application is of course framed by its own package.xml.  Assuming there are no conflicts between packages, it's pretty easy to get multiple applications deployed into a common dev org, but if your package.xml files use any form of wildcarding, you run the risk of cross-contamination if you attempt to round-trip changes through either FMT or the IDE (which drives back to the eternal question of when Force.com will support namespaces/packages!).

Is anyone else doing this?  If so, how are you solving this issue?  The naive answer is for each developer to have a dev org per application, but that seems really unwieldy.  It also makes integration testing across multiple applications more complex, likely requiring yet another org that's intended to contain multiple apps but never to be a read/write development sandbox.  I guess you could also have fully-qualified package.xml files, but that sounds even more unwieldy from an ongoing maintenance standpoint.

Thanks much for any thoughts you might be able to provide on this!