YAME also has CD emulation, but you will need to dowload the system card(s) to use it. As far as CD emulation goes it is a good as the Magic Engine, but it does not have Arcade Card support like the ME.
Hu-Go! is also a good emulator, but I would stay away from the the windows version (I haven't tried the latest one yet). I use both version 2.00 & 1.99 dos versions. I also had a little trouble getting it to work at first but after I messed around with the resolution setting in it's ini file it works perfectly now.