Thunderforce 3 - Sega Genesis/Megadrive. Also known as Thunder Spirits (SNES) and Thunderforce AC (arcade).
Fantastic sound fx, music, gfx combined with solid gameplay. Played it over & over & over again, which I can't say about any other shooter, except maybe Turrican 2. The difficulty ramped up pretty well, never *impossible*, plus the ability to switch weapons and ship speed provided a degree of tactical depth to the game.
A distant second place goes to Lords of Thunder on the Turbografx 16/SuperCDRom2. Incredible boss battles, incredible music, and graphics that even the SuperNES has seldom exceeded. (A version for the SegaCD/MegaCD was released which is almost as good, but the music seems to have really been 'cut down' from the Turbo version). The big problem though, is that even though you have the choice of 4 weapon systems, only one of them (Earth Armor) really packs the punch that you need to defeat the bosses.