Basically a prettier experience by default. If you've already customized Conemu to be prettier than default, you may not care, but if not, it is quite a difference. Also add Clink, which gives you a bunch of cmd tools that are defaults on Linux.
Anyway, neither of cmd or mysysgit is coming from cmder, and ConEmu has already made it straightforward to use these "add-ins". For me cmder is just a set of configs wrapping around ConEmu.