I'm starting a new thread on this since Google locked me out from replying.
Regarding conflicts using CVS, use SVN and tag certain files as requiring checkout. (I forget the procedure but it uses the property name you attach. You need to run a script on a regular basis that does this because it's done on a pre file basis.
Regarding which source control system. Any one should work (but I hate CVS). SVN is pretty nice.
Regarding which files should be archived (as source). I would not sweat it too much (e.g. files that get copied from library etc.) It's not the end of the world if they get versioned.
Ragarding binary: Just check them in as binary. SVN handles binary much better than svn and the database is amazingly small.
I'm still working myself on what makes sense for users. I have the CAD folks that use solid works working very nicely on SVN. If also saved their butts in short order.
I'm trying to understand where FPGA pin mappings are stored as the users claim they are in the db directory and other folks on the previous thread said never to version the db directory.