Do you happen to have a middle mouse button? Select the text you wish to copy, move the cursor to where you want to paste, and press the middle mouse button to do it. This works in X11 - X11 apps. OS X - X11 should work by copying as normal and then pressing the middle mouse button in the X11 app.
There might be a way to simulate the middle mouse button through a META key combo of some sort.
Some programs have copy/paste commands in the edit menu. You can try those, too.
IIRC, the X11 preferences also have some copy/paste stuff in there, but I could be wrong. I would check for you if I was at my OS X machine.