Just to clarify since I didnt mention at first. I mean 3D space shooters only... Like Wing Commander. 
(This isn't in response to previous replies, the ones mentioned very well may be 3D also, but I just don't want to hear a bunch of 2D scroller type games.)
In that case you're looking for the best space-opera game
What you're asking for by asking for best shooter is games just like that.. Disposable Hero, Xenon II Megablast, R-Type etc
(they're far more fun than Wing Commander by the way
)
