Of course there are vast differences in the two applications. I can't speak for security issues. I'm no tech princess, but from a user pov, this is what I've observed.

eMule has content Limewire hasn't. There is a greater variety of content. On the other hand, obtaining completed content on eMule sometimes requires zen-like patience. Content is downloaded sectionally. You may wind up with 56% of a file, but that 56% may be part of the beginning, the end, & 3/4 way through. It may take you a week or so of hopscotching through the server list to find the remaining 44%. During that barren week + (as with Limewire), you will note that no one has a problem finding what you have to offer. However, when you do connect, all the content which you haven't been able to find anywhere else is practically shoving each other out of the way to download. On the other hand, if a result in Limewire shows more than one source, you've pretty much got the completed content. Since people who use p2p generally tend to use more than one program, eventually everything gets everywhere. Its just nice to have the whole thing.

You need to be more tech-savy to use eMule than you do with Limewire. I had to test ports, do some configuring, retest, etc. But you're an eMule user, so you've done this. Limewire is so easy to use that, if you can use AOL, you can use Limewire. Much more user friendly.