The best one depends on your preference for discriminating against non-members of your download community, and protection from clients that are known to be unfriendly.
Note some of these unfriendly eMule clients have been banned from most eDonkey servers. However, the authors of those clients are rewriting the identification method so that they appear harmless, but in fact, they do not share at all or have the ability to kick off downloaders. Don't be tempted to try one of them, as you may get your computer blacklisted.
If distributing files, use one of the LSD mods, as they have "releaser" type of publishing, it connects to a different server every so often. Some of these have "community" and client exclusion settings to determine the acceptance of the client's connection.
It actually makes no difference what version you use for downloading, as the mechanism is pretty much the same across all the programs. The only difference is the method of publishing and transmitting to other clients.
Stick with the main versions of eMule if you're just downloading.
I have not tried Kademlia, as it does not run on my computers, all AMD.
If you'd like the added benefit of the Overnet system, download the eDonkey2000 hybrid version of Overnet. It adds a couple hundred or thousand more sources for your files.
Note: some ISPs are blocking common eDonkey ports such as 4662, due to the legal issues associated with P2P programs. Please select a port that is open, so you can recieve data from the servers. Don't be stupid and select an ISP-blocked port on purpose. You'll get blacklisted. To cover your ass from all that lawyer shit's that's caused a drop in use of P2P down to less than half the usage recorded a few months ago, and opened up crazy-ass businesses like http://www.MediaFence.com , get PeerGuardian from http://www.peerguardian.net It comes with a list of known P2P infiltrators from the media industry. The program works by scanning TCP/IP connections and dropping those on the blocklist, usually a list of known members that serve the media industry. With this in place, you won't get spied on. PeerGuardian is totally free of charge, and easy to set up. Note: PeerGuardian may block some media websites from loading, so be sure to turn off your P2P and PeerGuardian before visiting such sites. After your visit, you can turn on the PeerGuardian then your P2P program.