I keep seeing the following antipatterns or oversights happening in our codebase, most of them I believe we could mechanically check for.

No duplicate names in .project since it makes it impossible to import into Eclipse
bin folders should be svn:ignored and not be committed (causes problems when doing svn synchronization and all the .class files are showing up and some even commits it)
things in svn:ignore should be committed (either someone overrode svn:ignore or the svn:ignore were added later)
if pom.xml file exists target should be svn:ignored too.

Execution environment should be specified in manifest.mf's