Extensions that go into our main CVS should go in the extensions module. The MediaWiki distribution bundle is built directly from the phase3 module and should have a clean, empty extensions subdirectory.
At some point it would be nice to have more accessible releases of individual extensions...
I am still planning on evangalizing the mediawiki-agora (http://sourceforge.net/projects/mediawiki-agora), as a place where developers without core cvs access can develop extensions centrally. If anyone wants cvs access there, just let me know.
/Jonah