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Ninja Science Team Gatchaman - Yes, there's a shooter based on this anime, and yes, you play as the eagle-caped guys on foot (sort of like Elemental Master).

Ikari Warriors - Paul & Vince (no autoscroll, though)

Air Fortress - Spaceman (sometimes riding a sled-like thing, sometimes not)

Section-Z - Captain Commando

Forgotten Worlds - The Unnamed Ones (basically, an Arnold and Mr. T clone)

S.C.A.T. - I think this was a game that was trying to be like Forgotten Worlds. The characters are Arnold and Sigourney Weaver clones.

The Adventures of Dino-Riki - Dino-Riki is a caveman

Syvalion - A dragon

Dezaemon Kids - There were a ton of games on this that let you play as other things besides a spaceship. One example was a Lucky Neko.

Over Horizon - There's a code to turn your ship into a Samurai and the options into galloping horses.

Bio Hazard Battle - Even though the game shows a spaceship on the cover art, you actually select from four different flying insects to play as.

Silver Surfer