There's tons of things that can cause this. Here's some examples:
1) System restore turned on in the guest
2) hybrid disk drives (see other thread)
3) Antivirus software doing scheduled scans
4) Failing hard drives
5) starving the host for RAM or CPU
6) Time machine (make sure that you've excluded the VM from backups - they don't work anyway, and it'll cause this problem).
7) Missing or out of date VMWare tools.
and others as well.
If you're on 10.8, Fusion 5 has better support.