VMware Fusion Unity Mode – Hide Windows App Icons in Dock

You can try rebuilding your Launch Services Cache by running the following command in the Terminal:

sudo /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -domain local -domain system -domain user

The Launch Services Database is in charge of file/application associations.

Also, how did you uninstall VMWare Fusion - using the Uninstaller or just throwing away the application?

To use the Uninstaller (if you've just thrown away the application) you can run it either from the disk image you used to install VMWare (if you still have it) or open it from /Library/Application Support/VMWare Fusion. Once that is run it will remove all the helper tools VMWare uses to help integrate the virtual machines with the host operating system (in this case Mac OS X).

From Real separators for the Mac OS X Leopard dock:

Run the following commands from the Terminal:

defaults write com.apple.dock persistent-apps -array-add '{ "tile-type" = "spacer-tile"; }'
killall Dock

Once the dock restarts, you should see a blank space after the last application that is permanently in the Dock (before the icons for applications that are currently running but not always in the Dock).

You can now drag the empty spaces to where you want them, or right-click on them and select "Remove from Dock" if you no longer need them.