Dr. Robotnik's Mean Bean Machine (a.k.a. PuyoPuyo)

Oh, the hours I poured into this game. So much fun and so challenging in the later levels. Puzzle-gaming bliss!

EDIT: Of course I know how to use the Search function. :P

thats nr 19

94 :Arrow Flash

Drat! I thought I checked thoroughly enough. Ah well.

95: Splatterhouse 3

In my opinion, the best of the bunch thanks to its improved gameplay mechanics and branching storyline.

97 : Thunderforce Iv

just 3 more to go

Technically four more. You never fixed the number order after you pointed out my first submission was a duplicate.

And while I'm at it, here's another gem:

97: Rocket Knight Adventures

i have no idea what you are talking about o.o

98 : Haunting Starring Polterguy

This vampire cat is getting on my nerves...Why?! Why?! Why did you turned the knife in my old wound, reminding me how awesome was a Megadrive/Genesis back in the days?!

And here are another two games:

Wimbledon
Buck Rogers

Since nothing was posted anymore, I went and compiled the list, with the appropriate mobygames links.
It's in alphabetical order, with the suggestion numbers as an addition.

So, I suppose this is the official list of the 100 best Sega Megadrive/Genesis games, as voted by the GOG.com community:

Part 1/2:

Alien Storm (#040)
Altered Beast (#005)
Arrow Flash (#094)
Barkley: Shut Up and Jam 2 (#076)
Batman: The Video Game (#080)
BattleTech: A Game of Armored Combat (#066)
Battletoads (#023)
Beyond Oasis/The Story of Thor (#018)
Bonanza Bros. (#028)
Boogerman: A Pick and Flick Adventure (#087)
Buck Rogers: Countdown to Doomsday (#100)
Castlevania Bloodlines/Castlevania: The New Generation (#010)
Columns (#051)
Columns III: Revenge of Columns (#022)
Comix Zone (#006)
Contra Hard Corps/Probotector (#074)
Crack Down (#070)
Crüe Ball: Heavy Metal Pinball (#058)
Cyborg Justice (#072)
DEcapAttack: Starring Chuck D. Head (#026)
Desert Strike: Return to the Gulf (#075)
Dick Tracy (#032)
Disney's Aladdin (#031)
Double Dragon (#034)
Dr. Robotnik's Mean Bean Machine (#019)
Dune II: Battle for Arrakis (#038)
Dungeons & Dragons: Warriors of the Eternal Sun (#021)
Dynamite Headdy (#093)
Earthworm Jim (#060)
Ecco the Dolphin (#036)
Ecco: The Tides of Time (#004)
Eternal Champions (#045)
F-22 Interceptor (#063)
Fatal Labyrinth (#043)
FIFA Soccer 97 (#057)
Flink (#047)
Golden Axe (#008)
Gunstar Heroes (#013)
Haunting Starring Polterguy (#098)
Herzog Zwei (#052)
International Superstar Soccer Deluxe (#092)
Jewel Master (#082)
John Madden Football (#055)
Kid Chameleon (#030)
Landstalker: Treasure of King Nole (#044)
LHX: Attack Chopper (#069)
Light Crusader (#035)
Mega Bomberman (#053)
Mega Man: The Wily Wars (#059)
Micro Machines: Turbo Tournament 96 (#079)

Part 2/2:

Monster World IV (#027)
Mortal Kombat (#046)
Mortal Kombat II (#088)
Mutant League Football (#061)
Phantasy Star II (#024)
Phantasy Star III: Generations of Doom (#041)
Phantasy Star IV/Phantasy Star: The End of the Millennium (#002)
Pier Solar and the Great Architects (#073)
Populous (#083)
Ristar (#084)
Road Rash (#056)
RoboCop versus The Terminator (#012)
Rock 'n Roll Racing (#039)
Rocket Knight Adventures (#097)
Scooby-Doo Mystery (#054)
Shadow Dancer: The Secret of Shinobi (#015)
Shadowrun (#007)
Shining Force (#017)
Shining Force II (#062)
Shining in the Darkness (#014)
Shinobi III: Return of the Ninja Master (#037)
Soldiers of Fortune/The Chaos Engine (#090)
Sonic & Knuckles (#068)
Sonic the Hedgehog (#001)
Sonic the Hedgehog 2 (#016)
Sonic the Hedgehog 3 (#067)
Speedball 2: Brutal Deluxe (#065)
Splatterhouse 2 (#071)
Splatterhouse 3 (#095)
Street Fighter II': Special Champion Edition (#009)
Streets of Rage (#003)
Streets of Rage 2 (#025)
Streets of Rage 3 (#033)
Teenage Mutant Ninja Turtles: The HyperStone Heist (#011)
The Lost Vikings (#086)
The Ooze (#091)
Theme Park (#078)
Thunder Force III (#089)
Thunder Force IV/Lightening Force: Quest for the Darkstar (#096)
ToeJam & Earl (#029)
ToeJam & Earl in Panic on Funkotron (#085)
Two Crude Dudes (#042)
Vectorman (#050)
Virtua Racing (#049)
Wimbledon Championship Tennis (#099)
Wings of Wor/Gynoug (#020)
X-Men 2: Clone Wars (#077)
Zero the Kamikaze Squirrel (#048)
Zero Wing (#064)
Zombies Ate My Neighbors/Zombies (#081)

I really hope I didn't make a mistake.

the second half of the list

51: Columns
52 : Herzog Zwei
53 : Mega Bomberman
54: Scooby-Do Mysteries
55. John Madden Football
56: Road Rash
57: Fifa 97
58: Crue ball
59: Megaman The wily Wars
60: EarthWorm jim
61. Mutant League Football
62 : Shining Force II
63: F-22 Interceptor
64 : Zero Wing
65: Speedball 2
66: Battletech
67 : sonikku 3
68: LHX: Attack Chopper
69: Crack Down
70 : Splatterhouse 2
71 : Sonic & Knuckles.
72: Cyborg Justice
73 : Pier Solar
74: Probotector, a.k.a. Contra - Hard Corps
75: Desert Strike
76: Barkley Shut Up and Jam 2.
77 : X-men 2 Clone Wars
78: Theme Park
79 : Micro Machines Turbo Tournament 96
80: Batman
81. Zombies ate my Neighbours
82: Jewel Master
83 : populous
84: Ristar
85 : Toejam & Earl 2
86: The Lost Vikings
87: Boogerman
88. Mortal Kombat II
89: Thunderforce III
90. The Chaos Engine
91. The Oooze
92. International Superstar Soccer Deluxe
93: Dynamite Headdy
94 :Arrow Flash
95: Splatterhouse 3
96: Rocket Knight Adventures
97 : Thunderforce Iv
98 : Haunting Starring Polterguy
99: Wimbledon
100: Buck Rogers

and thats it !

100 megadrive games

or is it ?

101 : pete sampras tennis one fo the few j cart cardridges
102: sparkster the sequel to rocket knight
103: sonic spinball
104: tmnt tournament fighter ( the ai is off the cpu is unfair almost as bad as mortal kombat but it looks gorgeous )
105 : eternal champions ( its just so damn hard ! )
106 : batman returns
107: road rash II
108 : outrun
109 : outrun 2019
110: brutal paws fo fury ( and brutal it is )

lets see fi we can bring this 200

i twisted the knife a bit more by updating the list and positing to go to 200 ;p