You may be able to communicate to the clipboard by using xclip. You can use this python script here to do this job via communicating with 'dcop' and 'klipper' here. That is for KDE, I do not know how it would be done under GNOME... You may also be able to do this independantly of either GNOME/KDE by using DBUS, although I cannot say 100% confidently on that either...
Just be aware, that for a truly cross-platform job, you have to take into account of the different GUI's such as under Linux, X is the main window manager interface and either GNOME/KDE sits on top of it..I am not singling out other GUI's such as FluxBox, WindowMaker to name but a few, and that there will be a lot of platform dependant code, and also in conjunction, you will be dealing with Windows clipboard as well..all in all, a big integrated code...
Have you not considered looking at the raw X programming API for clipboard support? Maybe that might be better as I would imagine, GNOME/KDE etc are using the X's API to do the clipboard work...if that is confirmed, then the work would be cut out and be independant of the major GUI interfaces...(I hope that would be the case as it would make life easier for your project!)
Perhaps using compile-time switches, for each platform...WIN, KDE, GNOME, MAC or use the one that is already pre-defined..
Hope this helps,
Best regards,
Tom.