Anything with a dongle or physical hardware requirements (e.g. ASICS/GBICs).

Systems that stress RAM, I/O or CPU (e.g. heavily used databases).

Applications/Operating Systems where license/support agreements don't permit virtualisation (e.g. arguably Oracle on VMWare).

Anything mission critical that hasn't been properly tested in a virtual environment.

Anything on which your physical environment depends (e.g. door access control).

Anything on which your virtual environment depends (e.g. domain controller). If the virtual environment crashes and you can't logon to fix it because AD is hosted in that virtual environment, then you have a big issue.

Anything that must be secure (i.e. not accessible by the hypervisor admins).

Anything on which time sync is critical. Mitigate using NTP on all physical hosts.