If you've already extensively customized ConEmu, Cmder is probably just going to annoy you. It's ConEmu in portable app mode with different defaults and some bundled tools.
Cmder is a bundle of ConEmu, configuration files, a tiny launcher that makes ConEmu's portable app mode easier to manage, and some provisioning stuff for the unix tools and cmd enhancements.
I'd use Cmder if I needed to carry a complete environment around on a USB stick, but it's not difficult to set up something similar for a single system manually with ConEmu.
