No one has said it, so I'll do it:
The best NES shoot-em-up is Konami's frantic S.T.I.N.G.E.R. (Twin Bee).
I actually like the NES/Famicom Twin Bee's more than the later incarnations on PCE, SNES, etc.

There is something wonderfully raw about the NES/Famicom TwinBee's...the later incarnations are, in a way, too polished (too slick).
NOT THAT I DON'T APPRECIATE the 16-bit Twin Bee installments, of course.
S.T.I.N.G.E.R.