I haven't used VMware Fusion in a while, but this evening I noticed that applications from a Windows installation on Fusion 2.x were showing up in Spotlight.  At first Firefox (Windows) was the top hit for Firefox, trumping the OS X installation.

Not exactly what I was after.

It's simple to fix, although not terribly intuitive for someone who doesn't use Spotlight much (like me). Open System Preferences, and then open the Spotlight preference pane. Select the Privacy pane and drag your Virtual Machines folder in. By default this is located at \Documents\Virtual Machines\.

Close System Preferences and you'll find that your virtual machine contents will immediately be excluded from Spotlight.