I'm a web developer and I usually check out libraries and modules from
multiple different RCSes (SVN, CVS, Bazaar and Git) and then manage my project
with SVN (someday I'll switch to Git).  However Netbeans gets all confused about which VCS to use for any given file.  My experience is that if you have more than one RCS in a project NB will eventually screw up and choose the wrong RCS.

In Netbeans 6.8 and 7.0 I can just disable the CVS and Mercurial plugins, then use the CLI for working with those RCSes.  This works for my primary use-case.  However sometimes I work on projects that use one of those RCSes.  To be able to use NB in both situations I must manually dis/enable the appropriate plugin every time I switch projects.  

A better way would be to have the RCS selectable per-project.  The default could be "auto" where, just like it is now, NB makes a best-guess at what RCS to work with for any given file.  With the option of going into the project "Properties" window and choosing a specific RCS on the "Sources" tab.