Adventure Time: Hey Ice King, Why'd You Steal Our Garbage?!! for DS/3DS isn't a
perfect game because it's too easy/short but I COMPLETELY LOVE IT otherwise. It's a pure homage to Zelda II and
the soundtrack is amazing.
I Have No Mouth and I Must Scream for DOS might not be the greatest licensed game but IMO it's probably the most ambitious and deserves mention for that at least!
Indiana Jones and the Fate of Atlantis for DOS, a classic LucasArts adventure! I wish I could find my disc, I know I never beat all three paths...
Magic Knight Rayearth for Saturn, an excellent top-down action-RPG
Sam & Max Hit the Road for DOS is another LucasArts classic. (The Telltale sequels less so.)
Scott Pilgrim: The Game for XBLA and PS3 is a great beat-em-up! It made me aware of pixel artist Paul Robertson and the band Anamanaguchi, both are good things.
X-Men: Children of the Atom for Arcade/PS1/Saturn is probably the most noteworthy Marvel game that doesn't get talked about
nearly as often as the Marvel vs. Capcom series.
Zillion for SMS is a classic and I'm pretty sure most people are unaware it's based on an anime
I have fond memories of Beavis & Butthead and Garfield: Caught in the Act for Sega Genesis, but I'm not sure if they're really great games or if nostalgia is clouding my view. I don't know if I'd recommend them but I know I had a lot of fun with them when I was younger!