I split mine between one partition for windows and apps, and a separate partition for my vms. seemed a logical idea at the time, but really there isn’t much benefit in reality.
If you are into your disk encryption software then you might want to think it through a bit more. i use bitlocker and its fine for my needs. it does of course make it impossible to recover any data from a boot cd, but that’s the whole point.
i put my normal workfiles/documents to skydrive folder, and for any data in the vms, id just install a normal backup agent, as for the most part, the data contained within them is tiny compared to the actual vms size (os etc.). or setup a wee batch file to copy them off to a nas.
if your using vmware workstation, you can just drag and drop your vms to a fully fledged VC which could act as a sort of backup i guess.