Something that is getting on my (and others‘) nerves when using ported Linux-Software on Windows or Mac is the dependency of an X-Server. While under Windows – at least before Windows 7 – the integration into the rest of the Desktop-System was comparably good (depending on which Server you actually used), under Mac OS X you have a lot of compatibility-problems.
Of course, most programs should use GTK/QT, which is portable, but many of them still use low-level-interfaces to X11 (and some programs simply have old bindings for Motif, etc. – and besides that, sometimes you may even want X11.
Most of the Software uses the XLib. I wonder if its possible to create an XLib which implements most of the calls directly, i.e. has an „integrated“ X-Server inside itself which directly calls the System. Instead of having to connect to a Window-Manager, it could translate the given properties directly to the System. And – of course – every Application would have its own Context, so Things like the Dock in Mac OS X or the Window-Grouping under Windows would work, too.
There are a few problems with this – i.e. one would have to adapt some of the code of ported programs. But it should be possible to make that a lot easier.