Ranking of my favourite Progressive rock bands.

1. Genesis. Perfect mixture of emotion, story telling, and technical prowess. Their best progressive period is between 1971 until 1976.
2. Yes. Top level musicianship.
3. Rush. A little late in the game, but great non the less. Their best period is from 1974 until 1981.
4. King Crimson. They basically created the Genre in 1969 with "In the Court of the Crimson King". Lately, they have been sounding more like Tool. A very versatile band.
5. Marillion. Very similar to early Genesis. Their album "Misplaced Childhood", is my favourite single progressive album of all time. It is hard to believe this album came out in the early 1980's.
6. Gentle Giant.
7. Ven der Graaf Generator. Probably the least commercial and darkest of all the prog rock bands. There is nothing on earth like these guys. They are in a class of their own.

Other bands of note, but not quite prog in my opinion.
Pink Floyd. Great but more psychedelic rock than prog.
Radio Head. Their image is more alternative than prog but their album, "OK Computer" is pure genius. Paranoid Android has elements of Yes (the guitar solo) and King Crimson/Pink Floyd(the slow chanting section near the end of the track).