Have you had a look into Group Policy for deployment?
It is a little limited to .MSI files but almost any software can be made into a .MSI package by using free programs such as Winstall LE and a clean Virtual PC.
It won’t uninstall any software you currently have deployed in the wild but it can uninstall any software it has deployed.
This in conjunction with MDTS and WDS (both from microsoft and I think they are free) are very powerful tools.
To rebuild after a format using all of these tools it takes us 1.5 hours to do up to 30 machines at once back to full strength