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Well, the mime type issues, even for DnD, isn't as desperate as it sounds. Both KDE and GNOME understand MIME types and have their own MIME type databases; they also tend to use generally the same mime type settings for DnD, more so internally than between the various implementations. And therein lies the problem: each desktop has its own set of mimetype definitions. So if you use apps from just one desktop, or are selective in which apps you use, you have few to no problems.
What has been lacking is a MIME type database/registry and a set of standardized types for DnD (and by extension cut 'n paste) that everyone shares. FD.o is currently working on defining those standards. This is just like how FD.o has standardized other (meta)data registries and definitions, such as the .desktop file hierarchy or icon themes. This will lead to both better interop between the UNIX desktops as well as more consistency between individual apps as we'll then have a common deffinition to point to when some app get its wrong.
The UNIX desktop is coallescing (as opposed to fragmenting). Tomorrow's versions of KDE and GNOME will work even better together than today's versions. This seems to be the opposite direction that closed source systems generally go in, isn't it.