Not a very usual candidate, but the presentation of FIFA 97 was pretty damn spectacular on MD.

Pretty much the entire soundtrack of both Streets of Rage 2 & Revenge of Shinobi for me.

Barring music from franchises already mentioned (so no Sonic's Aquatic Ruin, Chrome Gadget or Shinobi III's Whirldwind) or arcade ports with lower quality music (so no Golden Axe 1, OutRun, Altered Beast, etc), and only one theme per game:

Many! But I'll give you my top 7...

7. Streets of Rage 2: Level 1-1 (Go Straight)

6. Mega Man: The Wily Wars - Mega Man 3: Wily Castle Boss Theme

5. Streets of Rage 2: Character Select

4: Columns - Clotho

3. Sonic the Hedgehog 1: Spring Yard Zone

2. Mega Man - The Wily Wars: Mega Man 2 - Wily Stage 1

1. Sonic the Hedgehog 2: Chemical Plant Zone

Can't believe no one mentioned these...

Thunder force series sound track

streets of rage 2

super shinobi

phantasy star 2 

Great game, too.  I posted my two favourites from TF III - The Grubby Dark Blue and Back to the Fire.

Well I can't think of too many memorable tracks unlike the c64, I did always like micro machines theme though.
https://m.youtube.com/watch?v=eIwJuHnJFvY

X-Men 2 Clone Wars
Adventures of Batman & Robin
Vectorman

*Mind blown

Oh yeah and genesis golden axe soundtrack is way better than arcade soundtrack.Seriously just watch both intros and hear for yourself.

Golden axe or Road Rash :) Oh those were fun and the music really helped :D