I've been running a Windows VM under Parallels on my work Mac. I have my home directory encrypted using FileVault. I've had ~5 lock-ups in the past 6 months where my Mac has just locked hard. It always seems to happen when I'm using a Windows VM. I've allocated 768 MB of RAM to the Windows VM. The Mac has 2 GB of physical RAM. The disk image is pre-allocated, to avoid performance problems with it being resized on the encrypted volume.
I've wondered if the box has locked up because FileVault cannot allocate memory for some reason. This doesn't seem to happen in normal usage. Maybe the Windows VM is pushing memory usage over the edge.
Today I've switched to hosting the Windows VM disk outside the encrypted partition, and using NTFS encryption for the data I need to protect. Hopefully that will work better.