The most visible difference is the packaging, I do build the LimeWire.app not using an installer application but using simple OS X app packaging so it is a simple drag and drop install. My different packaging also causes it to use JVM 1.4.1 instead of 1.3.1, but then I have not installed the official LimeWire in a while so I do not know if this changed already.

In the inside there are a few changes related to OS X specific things, like magnet URL support for both JVM 1.3.1 and 1.4.1. Otherwise most of the patches I did are already integrated in the mainline version.

Ah, yes and not to forget is one changed experimental menu item regarding repeated searches.