PaCifiST is the only Emulator that allows direct access to floppy drives.
http://atari.st/pacifist/
STEmulator does a decent job, and it is possible to have it running MiNT or MultiTOS. Want to try Geneva these days.
http://stemulator.net
Aranym is getting better and better - I think it has best capabilities to run MiNT and it can be used on Linux, Mac OS X and Windows.
http://aranym.sourceforge.net