UCS means Universal Chat Server, and it is included in all builds of EQEmu. The reason it is mentioned in the branch is because they are trying to incorporate an IRC connection into the UCS. It is at least partially functional, but I don't think they have everything in for it to compile under Linux or 64bit yet.
The Bots vs Instanced don't actually mean Bots or Instances as you are thinking of them. They are both referring to IRC connection types. One type is to make the client log on as an IRC bot, and the other lets them log in differently as an instance I believe. I don't really know much about IRC, so I may be a bit wrong about that, but that should be the basic idea of it. So, the branches that say IRC in them are both only for IRC related changes, nothing else.
I'm not exactly sure what the state of the entity upgrade branch is atm. I believe they are adjusting how the whole entity system works to make the entity lists handle better.
Unless you are wanting to play around with the IRC stuff, there isn't really any reason to build any of the current branches atm. You are best off to just stick to the trunk.
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