While CVS is the most widely used Version Control System in the open source community (and other communities), it has many glitches.

Subversion (http://subversion.tigris.org/) is a compelling replacement for CVS. Our company is looking into transitioning into it.

It should also be more friendly to JIRA, since log messages are stored per commit (and not per commit x every file); so an email-comment system like the current CVS mails would work much better (a single comment instead of tens of them); also the CVS integration in 2.6 would be much lighter due to the decreased log size (see issue JRA-3183)

Since Subversion interface has been kept close to CVS, my guess it's that shouldn't be too hard to implement suppport for it based on the current support for CVS.