scenario: ubuntu 9.04, FF, amule

(1.) Launch Firefox.

(2.) Then, insert about:config in the address bar. Right click on the list, select New, then Boolean; insert network.protocol-handler.external.ed2k as Preference Name and true as Value.

(3.) Now another right click, select New and String; insert network.protocol-handler.app.ed2k as Preference Name and /usr/bin/ed2k (or path to where the file is installed on you system) as Value.

(4.) Restart Firefox.

source: http://ubuntuforums.org/showthread.php?t=498713