Abadox should be mentioned. Flying sperm? Yes please!
Gradius has my vote, too. Gradius is quite possibly my favorite mega-series (i.e. especially taking into account games like Scramble, Life Force, Salamander, and Nemesis). I wouldn't like it as much (though would still rank it way up there) if it didn't have the atmosphere it does.
Definitely my favorite category. Some good new stuff in there I've not heard of, thanks for listing! Not a auto-scrolling shooter, but the arcade version of Alien Syndrome has some excellent bosses, in terms of surprises and grossness.
Making an action platformer with a transforming grappling hook: ChainStaff. Also made a shmup with multi-ships: Shoot 1UP DX, and more .
I don't know if I would call it a shmup in the strictest sense, but has anyone here played Compromised on the 360? It might be on Steam too.
It is more of a run n gun/shooter hybrid like In the Hunt since you control the scrolling. I remember enjoying it a lot when it came out. Fits creepy and surreal:)
MBG - There is a pretty decent twin stick version of Alien Syndrome for the PS2 on Sega Ages.