rxTools has a whole bunch of extra features like decrypting ROMs and stuff that Cakes and Reinand don't have (and don't need, really). Think of it like a CFW with Decrypt9 built in, sort of. Cakes and Reinand take the minimalism route, offering pretty much only a CFW/emuNAND with signatures patched (Reinand has a couple other things like a screenshot function, but it's not that important).
If you just want a CFW to run homebrew on or pirate games just get Cakes/Reinand. If you need a bunch of extra features then get rxTools.
Cakes/Reinand aren't region free by default, but you can use NTR CFW (a CIA you just run on top of Cakes/Rei) to get that.