Sonic fans
Nazo Unleashed Series
Final Fantasy Sonic X Series (Semi-Game) (No it's not a crossover, it just uses a FF-esque battle system)
Super Mario Bros Z Series
Full Metal Sonic (It's a Sonic Version of a FMA OP, but it's good for what it is.)
Sonic RPG Series (Semi-Game) (Not for me, but a lot of people like it)
Megaman Fans
Megaman/X: Final Battle Series (It's about what happens when both Classic Mega and X bump into each other, highly recommended if you want to 'fill the gap' between the Classic series and X.)
Bass' Revenge Series (Sequel to Megaman/X: Final Battle)
Hunter Zero Series (Sequel to Bass' Revenge)
Megaman Next-The Game (Fun Game)
Megaman X Next-The Game (Another Fun Game)
Fireman Incoming Storm (Game)
Megaman vs Airman (Great watch for those that know about the whole 'I can't defeat Airman' joke.)
Mario Fans
Super Mario Bros Z Series (This definitely goes without saying. lol)
Smash Bros X
Smash Bros X: Gaiden
Super GTA Bros
Super Mario Bros Crossover (Basically Super Mario Bros with the option to play as people like Mario/Link/Megaman/Samus/Simon Belmont/etc.)
I'm not that big on the Mario Flash, sorry.
Smash Bros Series
Brawl Taunts
More Brawl Taunts
Super Smash Flash (a Flash game based off of Smash bros with a good amount of Third Party Characters)
Brawl Is Here (Hilarious)
SSB:Brawl
Smash Kingdom
Smash Kingdom Melee
Smash Kingdom Lost Levels
Super Smash Bros ST series
Smash Bros X and Smash Bros X Gaiden
Others
Nin10Doh!
$00pah Nin10Doh! (NSFW)
Nin10DOH: ToThe64thPower (Recently Released)
Sprite TV series
Street Fighter Collab (NSFW on the Crimson Viper scene)
MK vs SF series (Street Fighter vs Mortal Kombat fights in possibly the best sprite fights not by Alvin Earthworm.)
Perfect Kirby series
Pokemon EX (short flash that's great for Pokemon fans)
More soon I guess. lol