Alright, enough of my chitter-chatter in this thread without actually contributing to it. Here's my list. I'm not putting in any rules like "only one game per franchise" or limiting myself to only one developer/publisher. I'm just listing the games that are my favorites across all systems I've owned. No limitations. These games I loved when they were new, and I still love them now. So here they are!
NES5.) Super Mario Bros.
4.) Super Mario Bros. 3
3.) Mega Man 4
2.) Wario's Woods
1.) Castlevania III: Dracula's Curse
Gameboy5.) Super Mario Land
4.) Castlevania II: Belmont's Revenge
3.) Mega Man V
2.) Pokémon Silver
1.) The Legend of Zelda: Link's Awakening
SNES5.) Starfox
4.) Mega Man X
3.) Donkey Kong Country 2: Diddy's Kong Quest
2.) Yoshi's Island: Super Mario World 2
1.) Chrono Trigger
Genesis5.) Columns
4.) Streets of Rage
3.) Splatterhouse 2
2.) Castle of Illusion: Starring Mickey Mouse
1.) Castlevania: Bloodlines
Virtual Boy5.) ???
4.) ???
3.) ???
2.) Mario's Tennis
1.) Virtual Wario Land
Nintendo 645.) Rush 2: Extreme Racing USA
4.) Super Mario 64
3.) The Legend of Zelda: Ocarina of Time
2.) The Legend of Zelda: Majora's Mask
1.) Super Smash Bros.
Playstation5.) Parappa the Rapper
4.) Street Fighter Alpha 3
3.) Final Fantasy VII
2.) Metal Gear Solid
1.) Castlevania: Symphony of the Night
Saturn5.) Tomb Raider
4.) Metal Slug (import)
3.) X-MEN vs Street Fighter (import)
2.) Devil's Castle Dracula X: Nocturne in the Moonlight (import)
1.) NiGHTS: Into Dreams...
Gameboy Color5.) Street Fighter Alpha
4.) The Legend of Zelda: Oracle of Ages
3.) R-Type DX
2.) Super Mario Bros. Deluxe
1.) Metal Gear Solid
Dreamcast5.) Skies of Arcadia
4.) Shenmue II (import)
3.) Shenmue
2.) Resident Evil: Code Veronica
1.) Soul Calibur
Gameboy Advance5.) Fire Emblem
4.) Metroid Fusion
3.) Mega Man Zero 4
2.) Castlevania: Harmony of Dissonance
1.) Street Fighter Alpha 3 Upper
Playstation 25.) Devil May Cry
4.) DragonQuest VIII: Journey of the Cursed King
3.) God of War
2.) Metal Gear Solid 2: Sons of Liberty
1.) Final Fantasy X
Gamecube5.) The Legend of Zelda: Twilight Princess
4.) Prince of Persia: The Sands of Time
3.) F-Zero GX
2.) Super Smash Bros. Melee
1.) Resident Evil 4
Xbox5.) Dead or Alive 3
4.) Ninja Gaiden
3.) Jet Set Radio Future
2.) Buffy the Vampire Slayer (don't you dare judge me!)
1.) Panzer Dragoon Orta
Nintendo DS5.) 999: Nine Hours, Nine Persons, Nine Doors
4.) The Legend of Zelda: Phantom Hourglass
3.) Elite Beat Agents
2.) Mario Kart DS
1.) Castlevania: Dawn of Sorrow
DSiWare5.) Asphalt 4: Elite Racing
4.) Cave Story
3.) Shantae: Risky's Revenge
2.) Dark Void Zero
1.) ART STYLE: PiCTOBiTS
Playstation Portable5.) Metal Gear Solid: Peace Walker
4.) WipEout Pulse
3.) Lumines II
2.) Castlevania: The Dracula X Chronicles
1.) Crisis Core: Final Fantasy VII
Wii5.) Punch-Out!!
4.) The Last Story (haven't finished yet, but I'm pretty sure it'll remain as one of my faves)
3.) Super Mario Galaxy
2.) Super Smash Bros. Brawl
1.) Tatsunoko vs Capcom: Ultimate All-Stars
WiiWare5.) Moto Heroz
4.) FAST: Racing League
3.) Castlevania: The Adventure ReBirth
2.) Mega Man 9
1.) World of Goo
Playstation 35.) WipEout HD
4.) Shatter
3.) LittleBigPlanet
2.) Metal Gear Solid 4: Guns of the Patriots
1.) SUPER Street Fighter IV: Arcade Edition
Xbox 3605.) Virtua Figher 5: Online Edition
4.) Banjo-Kazooie: Nuts & Bolts
3.) Sonic & SEGA All-Stars Racing
2.) Castlevania: Lords of Shadow
1.) SUPER Street Fighter IV: Arcade Edition
Nintendo 3DS5.) NEW Super Mario Bros. 2
4.) Resident Evil Revelations
3.) Kid Icarus Uprising
2.) Mario Kart 7
1.) SUPER Street Fighter IV: 3D Edition
eShop5.) Sakura Samurai: Art of the Sword
4.) VVVVVV
3.) Mutant Mudds
2.) Pushmo
1.) Mighty Switch Force!
Wow, that took longer than expected!