I love quite a bit of Shmups, but 3 I keep coming back to are these:
Beekyr - because the theme is so different, and it bring a breath of fresh air to the genre
Super Killer Hornet: Resurrection - Because Math Great game to brush up your math skills with I think
Sine Mora - Graphically stunning, and with a very complex, and rather sad story
Runner up being Syder Arcade, fantastic horizontal shmup!