One way to identify VMware systems is by their BIOS
BIOS ID: unknown BIOS Date: 10/16/01 BIOS Signon: unknown BIOS Type: PhoenixBIOS 4.0 Release 6.0 licensed to Intel Super I/O: unknown Chipset: Intel 440BX/ZX rev 1
another is finding files like:
Windows: VMware tools, under windows this will show up in "Add/Remove programs"
UNIX: ..such as /etc/rc.d/init.d/dualconf, "Copyright (C) 1998-99, VMware Inc." and the /etc/vmware-tools/ directory.