Here's mine...
1. DoDonPachi DaiFukkatsu - The best game in the best Cave series. I love the various arrange modes on the 360, and the game just oozes refined shmup design. Perfect.
2. Battle Garegga - Probably the most interesting and influential shmup ever made, and a hell of a lot of fun.
3. Lords of Thunder - My favorite 16-bit shmup and arguably the best soundtrack of any shmup ever.
4. Crimzon Clover - By far the best doujin game I've ever played, it feels like a lost cousin to the DoDonPachi series with a lot of interesting twists all its own.
5. Mushihimesama Futari - OMG the scoring system in this game is addictive. Brilliant design, beautiful aesthetics, and just another example of Cave at the top of their game.
6. Dragon Blaze - Easily the best Psikyo game. Complex and interesting system in an underused environment for the genre.
7. Truxton - My favorite Toaplan game, and one that can be enjoyed equally on the Genesis or on the arcade.
8. Ikaruga - Arguably the most fascinating thing Treasure has ever done, and one of the most devious mindfucks of a shmup ever concocted.
9. Gaiares - This was the first shmup I ever sunk serious time into (as a kid) and I still go back to it almost annually for the music, the large sprites, and the addictive weapon-stealing system.
10. Gradius V - The best game in a great series, and another homerun for Treasure.
As soon as I made this list I started feeling angsty about it as there are games I love that I think could easily be placed on here. I ended up only picking one game per series, though I probably could have put DoDonPachi and Gradius IV somewhere on a top 10 list too. Ibara probably should be in here, as should Dimahoo (both games I have love-hate relationships with).
This is hard, Mike! Please don't ask us to do this again for a while