CVSNT allows you to set a repository prefix (see http://www.idevelopment.info/data/Programming/change_management/cvsnt/PROGRAMMING_Creating_a_CVS_Repository_CVSNT.shtml). CVS repositories are then relative to the prefix. This avoids having to use C:\... style paths in your CVSROOT. In our case, our prefix is C:\cvsrepo. We then access the repository mentioned below with CVSROOT=:...:/web.

Jira's CVS integration balks at this though - I get "Error parsing cvs log: RCS filename 'C:\cvsrepo\web\module1/.cvsignore,v' does not start with the provided root '/web/module1'" when trying to add the module.

BTW: I can't use the full physical path (ie: CVSROOT=:...:C:\cvsrepo\web), as CVSNT won't allow this and returns "no such repository".