In gnome-terminal I can right click on a URL in the shell session output which gives me a menu that includes the "copy link address" option. But when I do that, nothing is copied into the paste buffer and the old data remains. Even pasting within the same terminal window still gets the old data (the desire is to be able to paste in anywhere). I also noticed this in Open Office. Is this just broken or does Gnome expect some special incantation to really copy the link address? This is under Ubuntu 9.10 desktop amd64. If I fall back to just doing a highlight on the text, then the text is copied (the text being the URL).

There are 2 clipboard buffers in Linux; one is with the mouse (mark text and paste it with the middle mouse button), and one is with the copy-paste features from the menus.

I think that the explanation to your problem is that you copied with the menus and pasted with the middle mouse button. After right-clicking a hyperlink and choosing "copy link address" you should paste by choosing the paste command from the menus and not by hitting the middle mouse button.