has a very nice sync facility. Easy to use. It displays exactly what will happen to each file before you commit. Optional subfolder inclusive. I've used it in FC for years and never banged my fist on the desk yet.
Note that FreeCommander is 32 bit. If you have a 64 bit OS some system folders may be subject to redirection. But I back up the system using an image backup program, not a file syncer.
I've also seen this one recommended. It looks very similar to the FreeCommander one. But I haven't tried it myself.