MD had the better sound. SNES had higher sample rate but the MD had proper bass-y synth that put hairs on your balls, and it had a frikkin headphone socket so you could listen to Streets of Rage 2 in stereo through your hi-fi while all your SNES friends were listening to Actraiser through a shitty tv mono speaker and putting moisturiser on and lame stuff like that.
Actraiser had much better music than Streets of Rage 2. Hrmz.
Graphically however I think I give the MD the nod. The MD had a much smaller color pallete, and lacked transparency effects. But other than that they were somewhat similar, with 15 colors per sprite. The SNES could have much more colors in the background, but at the end of the day the games still had to fit into tiny ROM chips, so for most games there wasn't much difference there.
In fact the genny often had more pallax stuff going on in the background.
Donkey Kong Country is perhaps one of the few non-mode-7 games that the MD would have trouble with, but the GBC port looked quite good so I'm unsure there. Toy Story and Vectorman showed that MD could handle CGI rendered images just fine.
The NES had a tiny color palette, didn't even have yellow!, but it still managed very colorful looking games, so I don't think that the 512 color palette is that big of a drawback for the genny. The SNES just had the bigger budget titles.
On the upside for the genesis it had square pixels. Also, the higher resolution meant that genesis games usually had a larger playing area. That's a significant advantage for side scrollers, especially twitch shooters. There was also less slowdown.
However audio is more important than graphics to me, and here the SNES had the MD soundly beat. Of course, music is more of a subjective thing. For me, the only genny game that had me stop and listen was the title screen of the non-cd version of Echo the tides of time. Phantasy Star IV had okayish music, but even the NES final fantasies were a step above.
One genny game that had me puzzled was Dune 2. I thought the MD had a better FM chip than the PC's adlib, but Dune 2's music sounds way better on the PC. Might be a result of cartridge space limitations though.
So I give genny the win on graphics and the SNES the overall win.