i was also just introduced to Beat Hazard which is not a traditional shmup (more like asteroids on a scrolling field) but it's one of the best games i've played in quite a while.
jamestown runs on linux so i got that as part of one of the humble bundles and i am really impressed with the quality of it. it's awesome playing a 16bit-esque game with proper scaling on a 1920x1200 monitor... hmm maybe i should try some of these games in portrait mode

anyone else into shmups? post your favorites here! i just got all the touhou games so i might start with those if i ever get a windows VM running.