RxTools is not worked on anymore while ReiNAND and Luma3DS are updated constantly.
They have kinda the same features,tho Luma3DS have some unique and specific features like:
-Language/region emulation
-GBA boot screen (man isn't that awesome?

)
-compatibility with a9lh
-other stuff that I don't remember right now... (look here!
www.github.com/AuroraWright/Luma3DS/wiki )
I believe RxTools has Regionfree too,I don't really remember