Is there a Pre-deployment Windows Workstation Verification Program?
I believe that the most recent version of SCCM can do checks based on users, whereas SCCM 2007 is purely computer based.
Given that, if you have some way, other than user, of organising your computers based on their use (which probably maps to users anyway) then you should be able to use SCCM Desired Configuration functions in SCCM to do all your checks. You should then be able to do some remediation based on results of your checks, or at least have a list of computers and problems to remediate.