At SATCHMO's request I made my own thread with my own list. Feel free to tell me what you think of it.
Criteria: The bands on this list are ranked by their influence, impact, originality and popularity. These criteria however are judged in the context of progressive rock, for example Pink Floyd would be number 1 if we were taking overall popularity, impact and influence into account. But instead the list is based on the influence and impact these bands have had within progressive rock, and how popular they are among prog fans.
For those of you who want to know how a band qualifies as progressive rock, see the prog ed thread. If you're too lazy to do that here's a brief definition. Prog is a very broad term (if both Fall of Troy and Rick Wakeman fall into the category, that's pretty damn broad) and much like punk and indie it's more of a philosophy than a specific kind of sound. An attempt to restructure rock music and put it into the plane of complexity and sophistication of classical music and jazz. Most prog bands have classical, jazz and folk influences, but just about any genre can get sucked into it, even punk.
Prog is usually associated with long, layered and complex compositions, ensembles of classically trained musicians, lyrical themes and ideas that are not familiar with most rock music (fantasy and deep philosophical themes for example), concept albums, the use of keyboards as lead instruments and various instruments unusual to rock music and of course an extremely high level of pretentiousness.
1. King Crimson
2. Yes
3. Pink Floyd
4. Genesis
5. Frank Zappa
6. The Moody Blues
7. Rush
8. Emerson, Lake & Palmer
9. Jethro Tull
10. Brian Eno
11. Can
12. Traffic
13. Mahavishnu Orchestra
14. Gentle Giant
15. Van Der Graaf Generator
16. Tangerine Dream
17. Hawkwind
18. Caravan
19. Marillion
20. Procol Harum
21. Roxy Music
22. Henry Cow
23. Mike Oldfield
24. Gong
25. Magma
26. Robert Wyatt
27. The Soft Machine
28. Wishbone Ash
29. Dream Theater
30. Uriah Heep
31. Hatfield & The North
32. Camel
33. The Strawbs
34. Porcupine Tree
35. Premiata Forneria Marconi
36. Renaissance
37. Focus
38. Art Bears
39. Colosseum
40. Amon Düül II
41. Barclay James Harvest
42. Queensryche
43. Univers Zero
44. The Mars Volta
45. Eloy
46. Tool
47. Pendagon
48. Muse
49. Alan Parsons Project
50. Faust
51. Ozric Tentacles
52. Fates Warning
53. Spocks Beard
54. Flower Kings
55. Peter Hammil
56. Neu!
57. Symphony X
58. Anglagard
59. Comus
60. Supertramp
61. Arena
62. Harmonium
63. Gryphon
64. National Health
65. IQ
66. Kayo Dot
67. Isis
68. Ayreon
69. Happy the Man
70. Nektar
71. Egg
72. Supersister
73. Coheed & Cambria
74. Pain of Salvation
75. Family
76. Khan
77. Fall of Troy
78. Oceansize
79. Riverside
80. Banco Del Mutuo Soccorso
81. Mostly Autumn
82. Dredg
83. The Nice
84. Echolyn
85. Le Orme
86. S.B.B.
87. Greenslade
88. Lucifer's Friend
89. Sleepytime Gorilla Museum
90. Klaatu
91. Magnum
92. Jade Warrior
93. Höyry-Kone
94. Picchio dal Pozzo
95. Kansas
96. Captain Beyond
97. Rick Wakeman
98. Liquid Tension Experiment
99. Goblin
100. Utopia
I also have a list of special honorable mentions. These are artists who have a decent amount of material that could be called prog, some of them were infuences on prog and others are influenced by it, but overall these artists are mostly associated with another genre or style, and are not commonly associated with prog.
SPECIAL MENTIONS:
Radiohead
Queen
Kraftwerk
The Residents
Captain Beefheart
Deep Purple
Talk Talk
Sigur Ros
Godspeed You! Black Emperor!
Electric Light Orchestra
Syd Barrett
Fairport Convention
Dixie Dregs
Return to Forever
Phish
Mr. Bungle
Vanilla Fudge
Arthur Brown
Primus
Ween
Super Furry Animals
dEUS
The Decemberists
Opeth
Mastodon
Between the Burried & Me
Iron Butterfly
Buckethead
Kate Bush
Peter Gabriel
Vangelis