Limit the number of versions time machine stores of particular files
Since you don't want no as an answer, and since Time Machine is proprietary software that you cannot modify you only have two options (don't complain, you asked for it)


convince Apple to implement the missing feature
implement your own version of Time Machine


You could modify backups from the terminal or with the Finder: backups are just directories with hard links but beware that you will most likely make them unusable by Time Machine (as Time Machine relays on the fact that the backups are as they were created).

There is a function in Time Machine "Delete all backups of" which removes backed up copies of a file. You could research if this is scriptable (Apple Script or terminal). I had no luck but seems the only way to periodically clean up a backup (with cron or similar)

You didn't specify which virtualization software you are using. If it's VirtualBox there is a workaround to reduce the size of the backed up data using snapshots: http://blog.matteocorti.ch/?p=331