The best CVS is CVS ;-)
I believe I use this version:
http://aminet.net/package/util/gnu/cvs-1.11.4I use CVS almost exclusively on Amiga projects, still - partly to avoid the effort of changing, partly for better software support.
But I suspect the question is more about 'version control' as a general concept.
It's hard to beat simple RCS if your needs are simple and only you are working on the code. I still use it for one project. I believe I use the version from ADE/GeekGadgets, so this:
http://aminet.net/package/dev/gg/rcs-binHowever perhaps the better version control system available to Amiga users is SVN:
http://aminet.net/package/dev/misc/subversion-1.1.4An old implementation, but if you're branching/merging needs are limited then totally suitable. I have been using this recently from the Amiga with a Sourceforge project.
Version control is something I believe a developer should learn as number 2 on their list (number 1 being "how to program"). It's nice to have the discipline when working alone, but is invaluable when you move to working in a team.