Badass platformers? If you look hard enough, you'll find some gems on HuCard
HuCard
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Ninja Spirit (my favorite ninja themed platformer on any console, hands down)
SonSon II (It's basically a cartoon graphics version of Black Tiger, which is awesome)
Jackie Chan Action Kung Fu
Bonk's Revenge (best of the three TG16 Bonk games, without question)
Bonk's Adventure
Daimakaimura (aka Ghouls N' Ghosts. SuperGrafx Hucard)
Ninja Ryukenden (aka Ninja Gaiden. Chunky parallax aside, still an awesome 16-bit graphics remake of the first Ninja Gaiden game)
Legendary Axe
Legendary Axe II
Mizubaku Daibuken (it's like Parasol Stars as a platformer game!)
Cadash (multiplayer arcade goodness with RPG-ish elements)
Legend of Hero Tonma (decent Irem platformer with insane firepower)
New Adventure Island (one of the best Adventure Island games on any system imo)
Madouou Granzort (SuperGrafx sequel-ish to Keith Courage)
CD games
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Akumajo Dracula X - Chi No Rondo (Should need no introduction. One of the greatest Castlevania games ever created)
Kaze Kiri (love it or hate it, it's a great game if you consider it in the same vein as games like Vigilante, etc.)
Mugen Senshi Valis (superb Super CD-ROM2 remake of Valis1. Probably my favorite Valis game on the PCE)
Valis III
Valis IV
Shubibiman 3 (a departure from the Megaman-ish feel of the 2nd game, and I consider that a vast improvement. Where they largely failed at cloning Megaman, they succeeded in creating an excellent hack-n-slash platformer with Shubibiman 3)
Dynastic Hero
Ys III (plays like Zelda II on the NES with more RPG-ish elements)
Shadow of the Beast (Better than the Genesis port, imo)
Chiki Chiki Boys (Dumb name, pretty fun game)
Blood Gear
Probably a ton of other CD games I can't think of off the top of my head
P.S., Bloody Wolf and KiKi Kaikai are NOT sidescrollers. They're both great, but both are overhead run-n-gun games like Commando or M.E.R.C.S.