[ From http://bugs.debian.org/469579 ]

"When a PDF file contains a URL link, right-clicking and selecting "Copy Link Address" only copies the link to the clipboard (i.e. I can use "Paste" in an edit menu or Ctrl+V in many applications to paste the content), but does not copy the link to the primary selection (i.e. I cannot paste the content to, e.g. xterm window by middle-clicking within the window). 

I do not think that this is an expected behavior, as most applications, such as IceWeasel, copies whatever content is in the clipboard also to the primary selection (e.g. if I right-click on a link and choose "Copy Link Location", I can paste the content elsewhere by middle-clicking, as well as the usual paste method). "

This seems to differ even between GNOME apps. Evolution for example, copies URLs to both the clipboard and primary selection. On the other hand, copying an URL from the Nautilus about box only copies it to the clipboard.