Out of the current, unmerged, branches:
- rathena : It's being kept for historical reference, but it is no longer updated now that rAthena is on GitHub (it'd be pointless and it'd make our repository even larger)
- zones : It was already there before I joined, so I know very little about it. I believe it's a dropped project favor of the HPM interfaces. Ind perhaps knows more about it than I do...
- bcrypt : Stalled until further notice. Gepard is on hiatus, and he's the branch author, even though I have contributed to it as well. I can consider resuming to work on it myself if there's enough demand, but there are some performance concerns that need to be solved/mitigated. It would also require a rewrite of the authentication (and brute-force mitigation) part in control panels or other third party software before being usable.
There are also other branches being developed, but they're not part of the main repository yet because they're not mature enough (some of us have branches in their own GitHub fork of the repository)
Edit: I forgot to mention, none of those branches has its history set in stone yet, so they should be only used if you know to recover your working copy from a history rewrite (rebase, etc)