The issue here is that a lot of lists i've seen on the internet over the years are marred by entries which were popular at the time because they were impressive for what they were - (shoddy) arcade ports, sports titles, and other questionable titles that i have no idea why they're listed as something good apart from the nostalgic feelings they evoke from the authors.
The Sega Mega Drive is action 2D scrollers incarnate, with a couple of excellent RPGs thrown on top. Here's what i think is the cream of the crop:
Phantasy Star IV
Shinning Force II
Thunder Force IV
Gaiares
Eliminate Down
Sonic 3 & Knuckles
Alien Soldier
Gunstar Heroes
Shinobi III: Return of the Ninja Master
Castlevania Bloodlines
Streets of Rage 2
Rocket Knight Adventures
Mega Turrican
MUSHA Aleste
Battle Mania Daiginjō
Panorama Cotton
Contra: Hard Cops (JP version is far more easier)
Here's what i think are great games to play once you're done with the cream of the crop:
Elemental Master
Alisia Dragoon
Thunder Force III
Sonic 2
Revenge of Shinobi
Beyond Oasis
Dynamite Headdy (recommend JP version with the
translation patch, the localization cut content out)
Gleylancer
Ranger-X
Ristar
Shining Force
Splatterhouse 2 & 3
Twinkle Tale