Absolutely,
I do this with all my projects (don’t check any IDE-specific files in, so someone using Textpad sees the same thing that someone using JBuilder sees).
1) Synchronize your project with CVS, make sure all changes are sync’ed up
2) Add web capabilities to your project, setup everything you need.
3) Resync with the CVS repo, add the .myeclipse directory, .mymetadata file and any other .my* files that are new as a result of adding web caps (adding other capabilities like Hibernate or Struts will add new dot files, so remember to handle them too) now add all these files to your .cvsignore file
4) All all new files to cvs ignore until the only new thing is the .cvsignore file itself, go ahead and check that in.
Now your computer will be the only one with the myeclipse-specific files. Each ME developer will need to add web caps themselves, but as long as the .cvsignore file is in the appropriate dir of your project (have them update to get it) then their clients won’t commit any of the ME-specific files into CVS.