I am sure that everybody here is aware of this, but I just like to point it out time to time to remind everybody. It's like trying to explain how Windows 98 sucked to people that used Windows 98 for 7 years or more... they often don't realize how crappy something is because they have lived with it and avoiding it's problems has become second nature.
In Linux on Gnome:
1. Open up Gnome-terminal. Highlight some text and right click, select copy. Highlight some other text.
2. Close out Gnome-terminal
3. Open up Gedit.
4. Middleclick to paste, then right click paste.
Notice how you have 2 copy-n-paste buffers. Highlighting text makes the first buffer go away and be replaced by new text. This makes it almost entirely worthless for anything except working with a terminal. Using middlelick copy is one of those habits I wish I can break myself from doing.
The second buffer works in a sane way.
5. Open up firefox. Highlight some text, Right click copy.
6. Close out firefox.
7. Attempt to paste text into Gedit.
Notice something wrong?
The only people that get it right are Gnome apps that religiously follow the HIG. Probably KDE-only apps get it right, too. Everybody else gets it wrong almost every single time. Some apps will clear everything out every time. Some apps will override one buffer with another in order to be helpful. All sorts of really weird and crappy behavior.
It's something that is fundamentally broken with X and has been since the beginning of time. I don't think there is any sane way to fix it as nobody has been able to do so. Even with aggressive clipboard managers it's still a bit hit or miss if it works sometimes.