LogFAQs > #885454804

This is certainly not all of the currently unmentioned ones but atleast a few more:
Action Pachio
Alfred Chicken
Ardy Lightfoot
Arnold/Tasuke and Sonya/Kyapiko from the Shockman/Kaizou Choujin Shubibinman series
B.O.B.
Big Nose the Caveman
Billy the Shell from Armadillo
Bub and Bob from Bubble Bobble
Bug!
Chuck D. Head from DecapAttack
Chuck Rock
Claw
Cookie from Panic Restaurant
Davy from Chameleon Twist
Dr Franken
Fargus and Nikki from Pandemonium!
Flink
Francesca/Doropie from Krion Conquest/Magical Doropie
Greendog
Hammerin' Harry
Harley from Harley's Humongous Adventure
Hebe from Utopia/Hebereke
Hermie Hopperhead
Hewlett from Magic Boy
High Seas Havoc
James Pond
Jazz Jackrabbit
Jelly Boy
Jerry from Smart Ball/Jerry Ball
Joe & Mac
Kid Chameleon
Kid Dracula
Kid Klown
Lickle from Little Samson
Lomax
Marina Liteyears from Mischief Makers
Marko from Marko's Magic Football
Master Higgins
Mohawk from Mohawk & Headphone Jack
Mr Bones
Mr Gimmick
Mr Nutz
Oscar
Pepper from Clockwork Knight
Pierre le Chef from Out to Lunch
Plok!
Prehistorik Man
Princess from Magical Pop'n
Puggsy
Pulseman
Putty
Radical Rex
Rascal
Robbit from Jumping Flash!
Rocket from Rocket: Robot on Wheels
Rocky Rodent
Rolo from Rolo to the Rescue
Ruff and Tumble from 40 Winks
Santa from Daze After Christmas
Snow Bros
Soccer Kid
Spanky from Spanky's Quest
Superfrog
Tam and Rit from Rod Land
Tempo
The Wizard Boy from Incantation
Tinhead
Titus the Fox
Wagan/Wagyan
Vectorman
Whirlo
Whizz
Wiz 'n' Liz
Yakopoo from Trip World
Zero the Kamikaze Squirrel (Aero the Acrobat spinoff)
Zool
and finally, Miles "Tails" Prower