Wine-doors is an application designed to make installing windows software on Linux, Solaris or other Unix systems easier. Wine-doors is essentially a package management tool for windows software on Linux systems. Most Linux desktop users are familiar with package management style application delivery, so it made sense to apply this model to windows software.
You can even add your own repos of your favorite Windows software.
I don't personally have a problem with including Windows programs in, for example, Universe, as long as they are Free Software (ie. they comply to the requirements for being in Universe).
I don't think there's much difference philisophically speaking between a Java program running in a Java VM and a Windows program running in WINE (I *DO* know the differences, but from a workflow point of view they are similar), so I wouldn't be against it (having WINE as a dependancy obviously).
I don't think that non-Free programs should be supported though, since it's the same with Linux programs.
The important point to realise is that Linux can run proprietary programs just as well as Free Software programs, and so can Windows. The focus, in my opinion, should be that as long as it runs then the license is the deciding factor.
There is a practical reason limiting this, which is that there are few Windows Free Software programs which don't run natively on Linux. The only ones I can think of are TurboCash and aTube Video Downloader. This shouldn't affect the main point though.
If someone is willing to package and maintain it, I have no problem.