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Im just wondering since i have been playing a lot of Alien 3 lately.

Had a cracking soundtrack and sound FX too.

Honorable mentions...

Road rash
Speedball 2100
Mercs
....
And prolly one other game i have missed out :(
Very hard to say, some of my favourite games were, Cobra Command, Sunset riders and Zombies ate my neighbours.
Chakan the Forever Man
Shadowrun
Toejam and Earl!

That game is in a genre of it's own.
Phantasy Star IV.
That's a tough one. NBA Jam was pretty ridiculously addictive, but I also killed a lot of time on Mortal Kombat II and Virtua Racing. I don't know why, but there's something about hitting that damned horse that was a blast. Also it was the first racing game I saw that had hidden nooks and crannies to explore.
I was mostly a SNES kid but I had a Genesis for a short while and I remember really liking Shining Force 2. Not sure I could replay it today though.

Sonic 2 of course was fun.
Shining Force 1&2, Street Fighter 2 Special Champion Edition, Landstalker, Shining in the Darkness, Streets of Rage, Shadowrun, Truxton, Thunderforce III. Just some off the top of my head.
Sonic 2, Streets of Rage 2, Golden Axe, Phantasy Star IV, Street Fighter 2 Championship Edition, Rings of Power... and many more I can't even think of.

It's been a long time since I owned a Megadrive.

In fact, I sold it and all my games to buy a better PC. That's when I knew I was a PC gamer!
Toejam & Earl 2: Panic on Funkatron. I know most people preferred the first but I absolutely loved the 2nd.
I would have to say M.U.S.H.A is the best. followed by the likes of the sonic series, shining series and the phantasy star series.
Shaq-Fu! But seriously folks, if you count Sonic 3 & Knuckles as a singular game since A) that was Sega's intention in the first place and B) they actually plug in to make one "super cartridge", then that's the one for me.
Shining Force 2
Not owning a Mega Drive myself I didn't play many games on the system. But I have fond memories of Streets of Rage 1 & 2 and Golden Axe.