I, for one, prefer the EGA version of Loom as the CD version only has music in the dialogue scenes. Which is, needless to say, annoying as it kills the athmosphere - the Blacksmith's Guild just ain't the same without the background music. Same goes for Crystalgard, etc., etc. ALSO, there are far less close-up scenes and half the gore is gone (especially noticeable in the Shepherds' graveyard towards the end of the game) which ruins the intended tension of the scene.
MI1 VGA is also debatable - the SCUMM Bar looks far crisper in EGA as it's not so damn dark in there. AAaaand so on.
Amen to that. MT-32. Nuff said. Even via DosBox's emulation, courtesy of MUNT (somehow, despite there being only one proper MT-32 emulation engine in the world, AFAIK, ScummVM's MT-32 emu sound sounds worse than DosBox's on the same machine on the same quality settings - what gives?), it still sounds far better than the (supposedly more) technologically advanced General Midi + 100+ meg-sized soundfont combo. Actually, barring MT-32, I've found myself reverting to AdLib emulation more and more lately...Later Sierra games that were released in 256 color for the PC are *definately* best on the PC.
The same goes for most LucasArts games as well - those that support MT-32 anyway. IJFoA becomes so much more vivid when Indy's whip finally sounds like a whip... and you can't deny that those custom lava-bubbling sounds in the end make it all even more fun and athmospheric