Continuous integration should run all your functional and performance tests if possible. Each "unit" (could be a commit or a push or a merge depending on your philosophy) can cause errors, and being able to pinpoint the unit in which the fail happened is immensely valuable.

If you have something really long running (eg you make a database and have a two week test), then you may be able to minimize your test (possibly automatically) and use git/hg bisecting to find it.

Fuzz testing (finding holes in your code) can be run separately, and again, you can find the root cause through minimization and bisecting.