Valve actually still has a full Quake engine license.
During the development of HL2, this allowed developers to start building levels while the engine itself was still in production. They then slowly replaced parts of it with the new engine.
I don't know what this means for licensees, but I imagine Valve's got some special deal with id. id has profited greatly from Valve, so I would imagine they bent over backwards for them.
For the record, I do feel bad for the Valve team but I think we're all getting our due dessert for not caring much about operating system security. Perhaps what we're paying for is the belief that 'security' is antipodean to openness. Or maybe people were just lazy and wanted to write word processors quickly. It's easy to criticize now, I'm safe to theorize about any ideal system that I might like to see. Too many engineers like to criticize with hyperbole instead of sitting down and building a new system or even give useful, non-obvious, suggestions. You have to watch out for those hyperbolizing engineers. The amount of bitching an engineer does negatively correlates to his ability to fix said problem. Put another way: Effective engineers build. Ineffective engineers complain.
Capability Security discipline teaches us that enforcable security is a side effect of good user experience (if I may be allowed to reword the 30,000 ft overview).
# — 12 October, 2003