It's best to describe my question with an example. If I highlight "linuxquestions.org" on my Chrome address bar using the mouse, make the right mouse click and choose Copy from the menu, then I'm able to paste "linuxquestions.org" string with the middle mouse button, SHIFT+Ctrl+V or with choosing the "Paste" from the application menu. Now if I will execute:

..then I copy string "test" to X clipboard. I can paste this "test" string with middle mouse button, but SHIFT+Ctrl+V or right-click menu "Paste" options still paste the "linuxquestions.org". I'm running GNOME 2.30.2.

Are there multiple clipboards which are not always in sync? Something like desktop environment clipboard and X clipboard?

From what I know, yes, at least 2 types of clipboard.
1st - working in all desktop environment (or almost all) - in fact it should be the X's one
- you just select the text to copy
- you paste it with the middle mouse button
2nd - working on some desktop environment like GNOME or KDE
- you select the text and press CTRL+C to copy
- you press CTRL+V to paste

You have also some other shortcuts like CTRL+SHIFT+C and CTRL+SHIFT+V which can be used in a terminal for example.
It seems to use the same one than 2nd above.

Emacs for example seemes to use an internal one (not one of the 2 above).

ok. Actually, screen(1) has it's own clipbord as well And vim. I guess then each application(from desktop environments to text editors) is technically capable to have it's own clipboard?

In addition, I found nice small utility parcellite, which is a GTK+(as I mentioned, I use Gnome) clipboard manager while xclip is for X clipboard.

Has anyone used desktop environment, which has no clipboard at all? I mean only the X11 clipboard is available.

//turned out, that both of those clipboard belong to X. Here is a nice article.