I'd say companies are less locked into Windows the OS and more so tied to binary compatibility with Windows products. I've been watching and using Wine since the project began, and it has made unbelievable progress in the last decade. Given a few more years, I wouldn't be surprised if it reached the stage of near perfect compatibility with Windows products. That coupled with the shift to more and more "cloud applications" spells big trouble for Microsoft.
Given the success of serious virtualization platforms like VMWare ESX I do think there is a long term danger of Windows becoming a rather thin shim between actual applications and the underlying "real" OS. Especially with the current "Best Practise" of every application running on its own dedicated server as everyone is terrified of the potential conflicts if you have more than one vendor application on the same instance of Windows.
If WINE actually does reach a point where it poses a serious competitive threat to Microsoft, I'd be very surprised if MS didn't file a massive lawsuit against WINE's developers + various distros to "protect their IP".
Microsoft is not just going to idly allow WINE to steal its userbase, even if WINE becomes 100% perfect and everything runs and works exactly as it would on Windows. MS has a lot of money and they will use all of it to keep Windows alive, whether that means pounding everyone involved in open-source with streams of litigation, buying off distributors (see EeePC), propaganda and FUD campaigns and whatever else.
MS already sees Linux as a threat, which is what the deal with Novell is about -- it was a proclamation to all Linux users that Microsoft isn't just going to let you stop giving them money. You either go through their approved vendor (through whom MS makes money) or you risk big SCO-esque (targeting users, not makers) lawsuits for patent infringement, etc.
To sum up, WINE is good and nice, but as soon as Microsoft perceives it as a real threat they are going to mobilize billions of dollars to put it down.
MS doesn't care about virtualization because you still have to buy Windows to use it.
