I think Landstalker is up there, mostly because it looks like the art was actually designed for a limited palette instead of having a "the artist worked in 24-bit color and dithered the output" kind of look (Genesis/MD only supports 9-bit RGB without black magic).
Reason for this choice was the incredible 3D effect backgrounds, the MegaDrive hardware was doing things that the Nintendo fanboys claimed were impossible on the Sega Machine. Shame it was never released outside Japan, but if y'all get the chance, please check this one out!
(Edited by segasonic at 4:25 pm on April 10, 2002)
Castlevania Bloodlines, Contra Hard Corps, Gunstar Heroes, Comix Zone, the list goes on and on! Gunstar Heroes is just great for maximum spritage and sound. Contra Hard Corps has awesome backgrounds and level designs that rivals the SNES version of the series in every way.
I think the best gfx on the megadrive are in Thunderforce IV as it has the best parallax scrolling I have seen in any game ever. The only problem with it is the slowdown when things get a bit hectic on screen.
The Adventures of Batman and Robin looked pretty good. Lots of explosions, scaling, screen was always swarming with enemies or their bullets. But it was overly difficult and got to long and monotonous.
At times Shadowrun had some really good graphics, though of course I love it for the gameplay. I agree Landstalker had pretty well-designed and colorful graphics. Even if the sound was designed to drive me mad, with all its bwoops and swishes and AAAGGGGHHCK! cries when the enemies died... Let's see, Streets of Rage 3, which had some pretty impressive arcade-like graphics (so did 2). Oh! The Lost Vikings had great very colorful graphics, and of course so did the Sonic series.
Now, I'm pretty surprised that nobody mentioned Phantasy Star IV.
So to sum up, everything mentioned by others plus Shadowrun, Streets of Rage 3, The Lost Vikings 1+2, Phantasy Star IV.