I just updated one of my ~amd64 machines and something in gnome is badly broken now. I'm about to update another ~amd64 machine but I'll do it one package at a time until I can identify the culprit.
The symptom is that every application icon I click on starts in the background but never appears on the gnome desktop :/ Almost like they're being displayed on a remote X server instead of my local machine. Weird.