Two from me:
Ys I & II -
While I like the original PC88 version, I love the TGCD one! I do find it interesting that the TG versions of the non-CD tracks sound VERY similar to the originals.
DooM -
IDKFA by Andrew Hulshult, hands down! The 80's/90's fusion that is the one by Gary Gritness is also good. I think IDKFA is what DooM would have sounded like if they had chosen CD audio instead of MIDI.