*Takes a deep breath*
Archer and Saber from Fate/Stay Night
Arcueid and Kohaku from Tsukihime.
Taokaka from BlazBlue
Earthworm Jim
Etna and Flonne from Disgaea
Mario, Wario, Peach, and Bowser
Sonic
Donkey Kong, Dixie Kong, and Diddy Kong
Chrono from Chrono Trigger
Kirby and Meta Knight
Kat & Ana, Jimmy T from Warioware
Fox from Starfox
Cammy, Dan Hibiki, Chun Li, and Ken from Street Fighter
Liu Kang from Mortal Kombat
Cyberdemon from DOOM.
SS Officer from Wolfenstein 3D
Duke Nukem
Dr. Wright from Sim City.
Pac Man and Ms. Pac Man
Marco and that one guy's name who escapes me at the moment from Metal Slug
Vic Viper, Lord British, and some other ships fighting one of the bosses from Parodius.
Reimu Hakurei, Suika, Remilia Scarlet, Hong Meiling, and Cirno from Touhou
Bill and Lance from Contra
Rayman
Lloyd Irving from Tales of Symphonia
Ayu Tsukimiya from Kanon
DIO (Brando) from JoJo's Bizarre Adventure
Kenshiro from Fist of the North Star (DIO and Kenshiro use sprites from one of the Jump fighting games)
Jazz Jackrabbit
Crash Bandicoot
Mallow and Geno from Super Mario RPG
Samus from Metroid
Zool
Megaman Zero, Bass, and Dr. Wily
Hulk
The Alien
Han Solo and Darth Vader from the SNES Star Wars games
Kanna and Misuzu from AIR (Both of them use Eternal Fighter Zero sprites)
The Teenage Mutant Ninja Turtles
Ness and his party from Earthbound
Knuckles, Tails, and Robotnik from Sonic
The Lost Vikings
Phoenix Wright
Sora and Axel from Kingdom Hearts
Yggdra from Yggdra Union
The Blue Falcom from F-Zero
Spiritia from Rosenkreuzstilette.
Worms.
And as for the first picture, I know at least some of them, but I'm not seeing anyone mention the Timber Wolf (Mad Cat for folks in the Inner Sphere) from the MechWarrior games.