Yeah, Application Usage logs could do it, but as dpertschi mentions, its a pain to make the output usable.
Another option would be an Extension Attribute that utilizes the power of the Spotlight API.
Try something like this against a system to see what it gives you. It pulls the Last Opened Spotlight information for VMware Fusion.app-
#!/bin/sh
FusionPath=$( mdfind "kMDItemCFBundleIdentifier == 'com.vmware.fusion'" | head -1 )
if [ "$FusionPath" != "" ]; then
result=$( mdls "$FusionPath" | awk '/kMDItemLastUsedDate/{ print $3,$4 }' )
else
result="VMware Fusion not installed"
fi
echo "<result>$result</result>"
On my Mac it returns:
<result>2013-06-28 20:48:47</result>
which incidentally is the perfect format for a Date type Extension Attribute. You can then build groups or queries based on Macs that haven't opened it within X number of days. This won't help you know if the user has active VMs in it but it will at least tell you that they've launched the application.
EDIT: And of course I'm completely forgetting that the Casper Suite comes with an Extension Attribute right in the templates that pulls all installed Fusion VMs as well. Take a look in Settings > Inventory Options > Inventory Collection Preferences > Extension Attributes. Then click the Add Extension Attribute From Template link and turn down the Virtualization list. Add in "VMware - Virtual Machine List" That should collect all the VMs on the Macs.
I think in conjunction with the last used EA I posted above, you should be able to build a report of machines with VMs that have been used recently.