Used to play Touhou (and its cousin Seihou) a lot, but I fell out of it after Mountain of Faith since I didn't like a lot of the changes. I kind of prefered Embodiment of the Scarlet Devil/Lotus Land Story/Mystic Square over the later games since I felt like the cards in later games were starting to bloating up and were being dragged out too long.
Also spent a fair amount of time with
x.x's Blue Wish series. As well as
Warning Forever. (I really ought to redownload them or see if I still have them on my thumb drive.
I was also probably one of the few who preordered and got Raiden Fighter Aces, Raiden 4, and Deathsmiles on release. And Castle Shikigami 3 and Blast Works were large factors into buying a Wii, though I have been too busy with other good games on the system to play them (and I think I liked CS2 better). Need to get some point cards to get Radiant SIlvergun, Trouble Witches Neo, and Guwange and some other stuff sometime.
Though I'm pretty bad at the genre and my only notable accomplishment is finishing Imperishable Night Extra stage.
iainmet: If you have a Commodore 64 emulator you could get Shoot Em Up Construction Kit (SEUCK), allows you to create them really easily and set backgrounds, waves and everything else. It is really dated though.
Wishbone: SEUCK was released for the Amiga too, you know. I'm actually surprised that nothing like SEUCK has been made since. Sure, there are lots of different game development tools, but none that are as simple to use for non-programmers as SEUCK was. If you do know of some, I'd love to know.
And yes, the Amiga was a veritable smorgasbord of excellent shoot-em-ups.
Dezamon series, though the interface is all in Japanese.
http://hardcoregaming101.net/dezaemon/dezaemon.htm Also Blast Works to some extent.