My mac crashed and I had to restore the entire machine from my latest timemachine backup. This restoration largely worked, except when I boot up VMWare Fusion, Fusion now tells me that it can't find any of the three VMs that I used to access. They simply appear with a giant question mark and a "file not found" message.It appears that my time machine backups were not backing up the VMs or the directory in which they used to live.
If there was an exclusion set in Time Machine and you have not properly backed up the Virtual Machines then you're out of luck! 
BTW... *It is a known fact that Time Machine is not 100% reliable backing up/restoring Virtual Machines under all circumstances/conditions. Also backing up Virtual Machines via Time Machine is disk/time intensive and wastes a tremendous amount of space for something that may be corrupt and worthless come time to restore it. At a minimum I would exclude Virtual Machines from Time Machine and with the Virtual Machines shutdown, not suspended, and VMware Fusion closed then manually copy the Virtual Machines Package(s) to an alternate location, preferably on to a different physical hard disk. Then keep the User Data that is stored within the Virtual Machine backed up off of the Virtual Machine on a regular basis so as to always have a current User Data Backup. If you have to restore a properly backed up Virtual Machine that is not as current at least you'll have a working Virtual Machine and current User Data to go forward with when you find out your Time Machine Backup of the Virtual Machine fails.
My question: Is there a way that I can interrogate fusion config to determine where it thinks those question mark files are supposed to be? It obviously knows that I once opened them, but now can't find the source files. Is the info about file location for each one of these question mark VMs stored in some kind of config file behind the scenes?
Of course the VMware Fusion App knew where the Virtual Machine were stored otherwise it couldn't open then in the first place! 
Generally speaking one can save a Virtual Machine any place one wants assuming one has full permissions and adequate disk space. By default, normal file based Virtual Machines are saved in "~/Documents/Virtual Machines".
If you click on the entry in the Virtual Machine Library it should show you a error message which includes the fully qualified pathname however if it doesn't the information is stored in the /Users/${USER}/Library/Preferences/com.vmware.fusion.plist file. In some case the .plist file is a binary file and requires a proper app to examine the file with, like Property List Editor if Developer Tools are installed. The Array in the com.vmware.fusion.plist file where the paths to the Virtual Machines are stores is "VMFavoritesListDefaults2" and if you do not have the Property List Editor installed you can use either PrefSetter or TextWrangler to examine the com.vmware.fusion.plist file. Of if you want to archive and attach the com.vmware.fusion.plist file to a reply I'll look at it and tell what it shows however if the Virtual Machine's were not restored by Time Machine I'd have to say it a moot issue anyway and you're going to have to rebuild them from scratch if you didn't make proper* backups to begin with.