I have no idea why I haven't installed xsel already. The help mentions a secondary clipboard. X has a secondary clipboard? Is there a way to paste that (like middle click for the primary)?
Following the old zero-one-infinity rule[1], X has an arbitrary number of clipboards; the most commonly used are PRIMARY (select+middle click), CLIPBOARD (usually C-c/C-v or edit→copy menus) and SECONDARY which, as far as I know, can only be pasted using applications that support it (e.g. xclip -o).
[1]: http://www.catb.org/jargon/html/Z/Zero-One-Infinity-Rule.htm...