I had a bit of a documentation challenge approaching the problem of writing phpunit test for extensions, mostly because many of the extensions do this very differently and the manual did not have any recommendations.
It appears many extension have custom bootstraping code ( somewhat hacky path discovery and manual loading of core mediawiki files, and don't necessarily register their tests in a consistent way.)
I wrote up a short paragraph of what I would recommend here: http://www.mediawiki.org/wiki/Manual:Unit_testing#Writing_Unit_Test_for_Exte...
If that makes sense, I will try and open up some bugs on the extensions with custom bootstraping code, and I would recommend we commit an example test tests/phpunit/suite.extension.xml file for exclusively running extension tests.
Eventually it would be ideal to be able to 'just test your extension' from the core bootstraper (ie dynamically generate our suite.xml and namespace the registration of extension tests) ... but for now at least not having to wait for all the core tests as you write you extension tests and some basic documentation on how to do seems like a step forward.
--michael