As far as I can see, the main case this covers is, for instance, say Apple adopts GPLv3 Bash. IBM decided to sue over their patent on causing the letter 'w' to be displayed on a computer screen (or whatever). Currently, Apple can do three things; fight it, settle, or stop using bash (the last is impractical, of course). This clause of GPLv3 almost removes the settlement option; IBM would be highly unlikely to license the patent to, not only Apple, but anyone redistributing the redistributable source from MacOS.
For a slightly more realistic example (most of the GPL stuff Apple uses, except for GCC, is not really all that vulnerable to patents), take the bluez Bluetooth stack, used by Android. There's a very real risk that one of the many holders of Bluetooth related patents may assert one against Google or against an OEM over bluez, and in that case, if the patent was valid, licensing it would be the obvious solution. This would work, because bluez is GPLv2; it wouldn't necessarily work if it were GPLv3.
I can see what the FSF was going for with this clause, but it does make it substantially riskier for companies to depend upon GPL(v3) components.
