So hard to think of just one, my mind tends to split up the games according to their platforms, so here's my choices:-
When i was thinking of my favourite i almost forgot this one, but there's something very special about missile command. The first time i played it was on the Atari 800xl, the cartridge was an unbelievable 8k. I mean how do you make a 8k game so playable, it's quite astounding. 8k wouldn't even get you an error message in windows hehe. When you think of all the gigabyte sized games around that are unplayable, this one puts it to shame.
The other game also on the Atari 800xl was Zybex by Zeppelin. This game is fantastic, It's one of the most intense shmups i've ever played. It also features some great music quite reminisent of david whittaker stuff.
So many on the c64, but i'd probably choose cybernoid 2 as the best overall shmup on that platform.
There was a lot of really tough shmups on the amiga, I'd probably choose stardust/disposable hero for the lovely graphics and addictive gameplay though.
And in the arcade nemesis was a firm favourite too. I lost a lot of money to this one.
Out of all these I'd probably choose missile command overall, which some of you might think is quite pathetic, given the graphics of some of the other stuff i mentioned, but the fact is, the gameplay is just so perfect, whether that was intended or was pure luck i can only guess...