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Season 1 - Episode 01 - Pilot
V1-D1T2/I2/P2/B2 - Big Yellow House (:00-:05) [Rename to "Opening"]
V1-D1T1/P3/B3 - Main Title A (:54)
V1-D1T2/I2/P2/B2 - Big Yellow House (:05-End)
V1-D1T3/I3/P4/B4 - Rain (3:29)
V1-D1T4/I4/P5/B5 - Exterminated (4:58)
Episode 02 - Gehenna
B6/P6 - Shorter Nights and Ashes (Gehenna) (:00-:02) [Rename to "Opening"]
B6/P6 - Shorter Nights and Ashes (Gehenna) (1:02-End) [Rename to "Create Desire"]
B6/P6 - Shorter Nights and Ashes (Gehenna) (:02-1:02) [Rename to "Arriving Home"]
V2-D1T8 - Dylan (4:36)
B7/P7 - Our 21 (Gehenna) (:00-:59.7) [Rename to "Ephesians 6:16"]
V2-D1T9/P7/B7 - Gehenna: Part I (6:43)
V2-D1T10/P8/B8 - Gehenna: Part II (3:05)
Episode 04 - The Judge
V2-D1T11 - Links (2:38)
V2-D1T12 - To the Hogs (6:27)
Episode 07 - Blood Relatives
V1-D1T5/P9/B10 - Mourners / Dragged In (3:24)
B11/P10 - Crossing Guard Finish (Wide Open) (4:51) [Rename to "Tina"]
B9/P11 - Never Stop Looking (Blood Relatives) (1:47) [Rename to "Mrs. Dechant"]
Episode 08 - The Well-Worn Lock
V1-D1T6 - Lock (2:41)
V1-D1T7 - Lock Part Two (:52)
Episode 10 - The Wild and the Innocent
V1-D1T8 - Death Prayer (3:30)*
Episode 13 - Force Majeure
P12 - Weed (:00-:01.7) [Rename to "Opening"]
V2-D1T14 - Hail Lauren (2:10)
V2-D1T15/P12A - Alignment (3:19)
V2-D1T16 - Pugilistic Attitude (1:57)
V2-D1T17/P12B/B12 - All His Children (6:32)
Episode 16 - Covenant
V2-D1T2 - Spinning (3:35)*
V2-D1T3 - Failing at Home (7:13)*
Episode 18 - Lamentation
V2-D1T4/P17/B13 - The Surgeon (3:32)
V2-D1T5/P18A/B14A - Alpine Page (2:17)
V2-D1T6 - Kidney Plate (5:20)
V2-D1T7 - Dude Looks Like A Lady (1:33)
B14B/P18B - Views (Lamentation) (2:10-End) [Rename to "The View"]
Episode 19 - Power, Principalities, Thrones and Dominions
B15/P19 - Fallen Angel (Powers, Principalities, Thrones and Dominions) (1:47) [Rename to "Sammael"]
B21/P20 - Always Someone (Paper Dove) (1:27) [Rename to "Murder in the Park"]
B16/P21 - Enough Love (Powers, Principalities, Thrones and Dominions) (:00-:42) [Rename to "Can’t Sleep"]
V2-D1T18/P21/B22 - The Ghost of Bletch (2:56)
V2-D1T19 - The Razor's Edge (4:49)
V2-D1T20/P22/B16 - A Unique Perspective (1:51)
Episode 21 - Marantha
V1-D1T9/I5/P13/B17 - Chernobyl (3:59)
V1-D1T10/I6/P14/B18 - Yaponchik (:58)
V1-D1T11/I7/P15/B19 - Myth No More / Antichrist (5:06)
V1-D1T12/I8/P16/B20 - Savior (7:47)
Episode 22 - Paper Dove
V1-D1T13 - Crushed Dove (1:56)
V2-D2T19 - End Credits (:37)
Season 2 - Episode 1 - The Beginning and the End
V1-D2T1/I1/P1/B1 - Main Title - Long Version (3:36)
V1-D1T14 - Headlights (2:52)
V1-D1T15 - Check / Get It Back Again (1:38)
Episode 4 - Monster
V1-D1T16 - Henny Penny (1:51)
V1-D1T17 - M-Files / Little Pigs (4:58)
Episode 6 - The Curse of Frank Black
V1-D1T18 - Jack O' Lantern (1:19)
V1-D1T19 - Battery (2:00)
V1-D1T20 - Acts (1:48)
V1-D1T21 - 790 Days (3:58)
Episode 8 - The Hand of Saint Sebastian
V1-D1T22 - Comatose / Origins / Woods (1:22)*
Episode 9 - Jose Chung's Doomsday Defense
V1-D1T24/I10 - Goopy (Alternate) (5:35)*
V1-D1T23/I9 - The Writer (2:52)
V1-D1T25/I11 - Final Chapter (1:39)
Episode 10 - Midnight of the Century
V1-D2T2/I12 - Delete (1:37)
V1-D2T3/I13 - Branches / Angels (4:52)
I14 - Bumper 4M2 (4:27) [Rename to "Reconciliation"]
Episode 12 - Luminary
V2-D2T1 - Stars (1:04)
V2-D2T2 - Journey North (2:08)
V2-D2T3 - Northern Lights (6:47)
V2-D2T4 - Rescue of Ventoux (5:35)
Episode 15 - Owls
V1-D2T4 - Damascus (4:35)
V1-D2T5 - The Subject (3:40)
V1-D2T6 - Aerotech (1:33)
Episode 16 - Roosters
V1-D2T7 - Trail (1:14)
Episode 19 - Anamnesis
V2-D2T8 - The Sermon (4:00)
V2-D2T9 - The Read (3:03)
V2-D2T10 - M. Magdalene (2:21)
V2-D2T11 - The Circle (2:49)
V2-D2T12 - Divine Daughter (9:42)
Episode 21 - Somehow Satan Got Behind Me
V1-D2T8 - Alarm (1:46)
V1-D2T9 - X-Fyles (2:04)*
V1-D2T10 - Sympathy of the... (2:02)
Episode 22 - The Fourth Horseman
V2-D1T13 - The Bleed (3:33)
Episode 23 - The Time Is Now
V1-D2T11/I15 - Hot Birds (1:32)*
V1-D2T12/I16 - The Peter Principle (3:07)
V1-D2T13/I17 - Catherine (2:29)
V1-D1T26/I22/P23 - End Title (:33)
Season 3 - Episode 4 - Closure
V1-D2T14 - Silence is Golden (3:08)
V2-D1T1 - Main Title (:54)
V1-D2T15 - Candy (7:27)
Episode 7 - Through A Glass Darkly
V2-D2T13 - Van Man (3:11)
V2-D2T14 - The Trailer (2:55)
V2-D2T15 - East... West (3:15)
V2-D2T16 - St. Max (7:33)
Episode 9 - Omerta
V1-D2T16/I18 - Santos Elves (3:50)
V1-D2T17/I19 - Unwrapped Gift (2:47)
V1-D2T18 - Love Jordan / Hobbit House (2:19)
V1-D2T19/I20 - The Way It Was (3:53)
Episode 12 - The Sound of Snow
V2-D2T17 - Guilt (1:50)
V2-D2T18 - Can't Let Go (6:42)
Episode 19 - Seven and One
V2-D2T5 - The Secret (4:06)
V2-D2T6 - False Alarm (2:21)
V2-D2T7 - The Light in the Water (8:18)
Episode 22 - Goodbye to All That
V1-D2T20 - Shrapnel (3:53)
V1-D2T21 - Channel 14 (4:14)
V1-D2T22 - Locked Out (1:21)
V1-D2T23/I21 - Drilling (4:51)
V1-D2T24 - End Title (:45)
V2-D2T20 - I Made This / 20th Century Fox Fanfare (:09)
Bonus Track:
V1-D2T25 - Main Title - Vocal Remix (:50)
* = Partially / Completely Unused
B = Bootleg
I = iTunes Release (2003)
P = Composer’s Promo
V1-D1/D2 = Volume I (2 Disc) (2008 & 2015 Releases)
V2-D1/D2 = Volume II (2 Disc) (2015 Release)
Note: Previous track order posted by fommes at http://jwfan.com/forums/. There are other main/end titles on the bootleg that are a combination of DVD rips that are not listed above.