The only noteworthy difference between version 1.6 and SourceForge version 1.5 beta 3 seems to be the end-to-end encrypted PM feature of 1.6. I can imagine situations where some special small group members might wish for another layer of trust like that but for normal filesharers the feature seems quite useless. The basic need for a filesharing group is to protect the network from hostile outsiders; version 1.6 protects private communications of group members A and B from a curious group member C that would have to use a modified client to spy PMs of A and B that happen to be routed through C - a rather hypothetical threat, especially as no developer has made such modified clients available so far.
As for the differences between Justin Frankel's original version and SourceForge 1.5b3 version, I think there are a couple of practically meaningful new features on 1.5b3 that make me recommend it to new groups instead of the original version. First: the new stealth mode, which encrypts the initial handshaking routines of WASTE clients when they connect to each other. This makes it harder for hostile third parties to detect that you are using WASTE in the first place - which might help you to avoid e.g. p2p traffic shaping at your ISP. Second: longer chat messages. This may sound like a small thing but anybody who has used the original client any longer knows how annoying it can be when your chat message is cropped but you are not aware of it. I think the original client allowed some 256 characters in a chat line, the 1.5+ versions allow 1024. 1.5b3 also has a nice broadcast feature that allows you to send a message to all group members (just open a chat channel named $$broadcast and send messages there).
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