Due to popular demand, I'm going to go ahead and post this topic. I'd like to keep it fairly small, so I'm limiting us to the two big series. Also, I know almost nothing of the others. So here's a working list. Let me know if I missed anything!
NES
MM1 - Complete?
MM2 - Bubble Man Stage, Heat Man Stage, Metal Man Stage, Enemy palettes (and maybe frames?)
MM3 - Gemini Man Stage (Normal & Doc Robot), Hard Man Stage, Shadow Man Stage (Normal & Doc Robot), Spark Man Stage (Normal & Doc Robot), Bosses (Yellow Devil is missing teleporting sprites, for one), enemies (Palettes? Sprites?), Gamma, Wily
MM4 - Dive Man Stage, Dust Man Stage, Skull Man Stage, Toad Man Stage, Enemies (Ring/Toad/Bright Man)
MM5 - Wily Stages, Wily Bosses, Wily, Enemies(?)
Bosses: Big Pets, Circling Q9, Wily Machine, Wily Capsule
MM6 - Bosses, Wily, Enemies (?)
Bosses: Rounder II, Power Piston, Mettonger Z, X Crusher, Mechazaurus, Tank CSII, Wily Machine, Wily Capsule
Wily & Light's Rockboard - all character's sprites
SNES
MM7 - Honestly, a lot here probably needs to be redone. We need all the stages, Enemies,
Bosses - Shirokumachine GTV, King Gojulus, Van Pookin, Shade Man Prototype Miniboss, Truck Joe, HannyaNED², Wily Machine, Wily Capsule
MM&B - All NPCs, Enemies, Minibosses, and Bosses. Also stages. Really, anything would be helpful.
MM Soccer - Wily's select icon, which may involve hacking.
MMX - Enemies could probably use a once-over. Sting and Boomer's Stages.
MMX2 - Bubble Crab all stages, all enemies.
Bosses - Giant Mechaniloid CF-0, Chop Register, Pararoid S-38, Magna Quartz, Serges (fortress), Agile (fortress), Neo Sigma
MMX3 - All Stages from the final and beta versions, Ride Armors, Probably more.
Bosses - Mega Man X3: Shurikein, Worm Seeker-R, Hell Crusher, Hotareeca, Press Disposer, Volt Kurageil, Vile MK-II, Dr. Doppler, Sigma, Kaiser Sigma, Some minibosses are different.
(Check White Jet's post below for more info)
PS1
MM8 - All Robot Masters, Stages, Enemies, NPCs, Wily
MMX4 - X and Zero and their upgrades, Cyber Peacock, Frost Walrus, ALL enemies,
Tentoroid, Eyezard, , Iris, General, Reaper Sigma, Sigma, Slime/Cyborg Sigma
MMX5 - X and Zero and their upgrades, Mattrex, the others. More info needed.
Sigma Head, U-555, Prism Guardian, Dynamo, Shadow Devil, Maverick Zero, Sigma, Final Sigma W
MMX6 - X and Zero and their upgrades, Blaze Heatnix, All Enemies.
Nightmare Snake, Illumina, Nightmare Mother, Gate, Sigma, Giant Sigma
Game Boy
Mega Man: Dr. Wily's Revenge: Wily Machine
Mega Man II: Enemies, Wily Machine
Mega Man III: Enemies, Dive Man, Drill Man, Dust Man, Skull Man, Giant Suzy, Wily Machine
Mega Man IV: Enemies, Charge Man, Crystal Man, Napalm Man, Stone Man, Satellite Cannon, Ballade, Bridge, Wily Robo, Wily Capsule
Mega Man V: Complete
Mega Man Xtreme: Enemies
Mega Man Xtreme 2: Enemies
Other
MM9 - All Robot Masters, Bosses, Enemies, and Stages.
MM10 - All Enemies and Bosses
Mega Man: The Power Battle - Wood Man, Heat Man, Gyro Man, Napalm Man, Cloud Man, Junk Man, Slash Man, Shade Man, Turbo Man, Yellow Devil, Van Pookin, Wily Machine
Mega Man 2: The Power Fighters - All Robot Masters and fortress bosses
Wily Wars (Gen):
Mega Man: The Wily Wars: Mega Man: Complete
Mega Man: The Wily Wars: Mega Man 2: Enemies
Mega Man: The Wily Wars: Mega Man 3: Enemies
Mega Man: The Wily Wars: Wily Tower: Fire Snakey, Buster Rod G. (without staff)
Rockman & Forte: Mirai kara no Chousensha: Enemies, Bosses, R-Shadow
Rockman Battle & Fighters: Mad Grinder, Mecha Dragon, Yellow Devil, Wily Machine
Did I miss anything else? Everyone, join! Let's give Megaman the anniversary Capcom wouldn't!
NES
MM1 - Complete?
MM2 - Bubble Man Stage, Heat Man Stage, Metal Man Stage, Enemy palettes (and maybe frames?)
MM3 - Gemini Man Stage (Normal & Doc Robot), Hard Man Stage, Shadow Man Stage (Normal & Doc Robot), Spark Man Stage (Normal & Doc Robot), Bosses (Yellow Devil is missing teleporting sprites, for one), enemies (Palettes? Sprites?), Gamma, Wily
MM4 - Dive Man Stage, Dust Man Stage, Skull Man Stage, Toad Man Stage, Enemies (Ring/Toad/Bright Man)
MM5 - Wily Stages, Wily Bosses, Wily, Enemies(?)
Bosses: Big Pets, Circling Q9, Wily Machine, Wily Capsule
MM6 - Bosses, Wily, Enemies (?)
Bosses: Rounder II, Power Piston, Mettonger Z, X Crusher, Mechazaurus, Tank CSII, Wily Machine, Wily Capsule
Wily & Light's Rockboard - all character's sprites
SNES
MM7 - Honestly, a lot here probably needs to be redone. We need all the stages, Enemies,
Bosses - Shirokumachine GTV, King Gojulus, Van Pookin, Shade Man Prototype Miniboss, Truck Joe, HannyaNED², Wily Machine, Wily Capsule
MM&B - All NPCs, Enemies, Minibosses, and Bosses. Also stages. Really, anything would be helpful.
MM Soccer - Wily's select icon, which may involve hacking.
MMX - Enemies could probably use a once-over. Sting and Boomer's Stages.
MMX2 - Bubble Crab all stages, all enemies.
Bosses - Giant Mechaniloid CF-0, Chop Register, Pararoid S-38, Magna Quartz, Serges (fortress), Agile (fortress), Neo Sigma
MMX3 - All Stages from the final and beta versions, Ride Armors, Probably more.
Bosses - Mega Man X3: Shurikein, Worm Seeker-R, Hell Crusher, Hotareeca, Press Disposer, Volt Kurageil, Vile MK-II, Dr. Doppler, Sigma, Kaiser Sigma, Some minibosses are different.
(Check White Jet's post below for more info)
PS1
MM8 - All Robot Masters, Stages, Enemies, NPCs, Wily
MMX4 - X and Zero and their upgrades, Cyber Peacock, Frost Walrus, ALL enemies,
Tentoroid, Eyezard, , Iris, General, Reaper Sigma, Sigma, Slime/Cyborg Sigma
MMX5 - X and Zero and their upgrades, Mattrex, the others. More info needed.
Sigma Head, U-555, Prism Guardian, Dynamo, Shadow Devil, Maverick Zero, Sigma, Final Sigma W
MMX6 - X and Zero and their upgrades, Blaze Heatnix, All Enemies.
Nightmare Snake, Illumina, Nightmare Mother, Gate, Sigma, Giant Sigma
Game Boy
Mega Man: Dr. Wily's Revenge: Wily Machine
Mega Man II: Enemies, Wily Machine
Mega Man III: Enemies, Dive Man, Drill Man, Dust Man, Skull Man, Giant Suzy, Wily Machine
Mega Man IV: Enemies, Charge Man, Crystal Man, Napalm Man, Stone Man, Satellite Cannon, Ballade, Bridge, Wily Robo, Wily Capsule
Mega Man V: Complete
Mega Man Xtreme: Enemies
Mega Man Xtreme 2: Enemies
Other
MM9 - All Robot Masters, Bosses, Enemies, and Stages.
MM10 - All Enemies and Bosses
Mega Man: The Power Battle - Wood Man, Heat Man, Gyro Man, Napalm Man, Cloud Man, Junk Man, Slash Man, Shade Man, Turbo Man, Yellow Devil, Van Pookin, Wily Machine
Mega Man 2: The Power Fighters - All Robot Masters and fortress bosses
Wily Wars (Gen):
Mega Man: The Wily Wars: Mega Man: Complete
Mega Man: The Wily Wars: Mega Man 2: Enemies
Mega Man: The Wily Wars: Mega Man 3: Enemies
Mega Man: The Wily Wars: Wily Tower: Fire Snakey, Buster Rod G. (without staff)
Rockman & Forte: Mirai kara no Chousensha: Enemies, Bosses, R-Shadow
Rockman Battle & Fighters: Mad Grinder, Mecha Dragon, Yellow Devil, Wily Machine
Did I miss anything else? Everyone, join! Let's give Megaman the anniversary Capcom wouldn't!