It depends on what you're trying to do.
If I were going to repackage my MAME collection, I'd most certainly use cmpro, since that's pretty much what it was built around.
If I were going to rename a bunch of NES roms to no-intro names, I'd use romcenter.
I like romcenter because it's more interactive and you can see the list of roms and what it wants to do to them, where's cmpro is basically blind and pray that it does what you think it does.
I've never tried to do any MAME stuff in romcenter.
I'm currently playing with a .dat file for a large collection of 80's DOS games that was recently released, and neither cmpro or romcenter are really built for working with anything other than roms, so I may have to write a 3rd option.