For MLdonkey, supported protocols are ed2k:, magnet: and sig2dat:, as well as BitTorrent links. For eMule and aMule, only ed2k: is supported, of course.
Please note that eMule and aMule support is still beta and has only been tested to work with eMule versions 0.45* and 0.46a, as well as aMule version 2.1.3, respectively. Also note that current authentication support for both is insecure! Passwords are sent in plain.