http://forums.tweakguides.com/archive/index.php/t-1769.html
I found the list at the following location.
http://www.midwinter.com/lurk/countries/master/eplist.html
This is the sequence JMS recommends, and following it adds to the story line.
Due to production constraints and other factors, several episodes during the run of the series were delayed, shown later in the sequence than originally intended. The effect isn't major in most cases, but there are minor things that make more sense if the episodes are viewed in the intended order. JMS has given the ordering for seasons one and two his blessing.
This list also inserts the TV movies into their proper chronological order; for example, "Thirdspace" takes place in the middle of season four.
Departures from the original US airing order are emphasized **. The number in the brackets refers to the disk and then the episode on that disk. The episodes with M are the movies.
Pilot Movies
1. (M.2) Babylon 5: In the Beginning
2. (M.1) The Gathering
Season One ("Signs and Portents")
1. (1.1) Midnight on the Firing Line
2. (1.2) Soul Hunter
3. (1.3) Born to the Purple
4. (1.4) Infection
5. (2.1) The Parliament of Dreams
6. (2.2) Mind War
7. (2.3) The War Prayer
8. (2.4) And The Sky Full Of Stars
9. (3.1) Deathwalker
10. (3.2) Believers
11. (3.3) Survivors
12. (3.4) By Any Means Necessary
13. (4.1) Signs and Portents
14. (4.3) ** Grail
15. (4.4) Eyes
16. (5.2) ** A Voice in the Wilderness part 1
17. (5.3) A Voice in the Wilderness part 2
18. (5.4) Babylon Squared
19. (6.1) The Quality of Mercy
20. (4.2) ** TKO
21. (5.1) ** Legacies
22. (6.2) Chrysalis
Season Two ("The Coming Of Shadows")
1. (1.1) Points of Departure
2. (1.2) Revelations
3. (1.3) The Geometry of Shadows
4. (1.4) A Distant Star
5. (2.1) The Long Dark
6. (2.2) A Spider in the Web
7. (2.4) ** A Race Through Dark Places
8. (2.3) ** Soul Mates
9. (3.1) The Coming of Shadows
10. (3.2) GROPOS
11. (3.3) All Alone in the Night
12. (3.4) Acts of Sacrifice
13. (4.1) Hunter, Prey
14. (4.2) There All the Honor Lies
15. (4.3) And Now For a Word
16. (5.1) ** Knives
17. (4.4) ** In the Shadow of Z'ha'dum
18. (5.2) Confessions and Lamentations
19. (5.3) Divided Loyalties
20. (5.4) The Long, Twilight Struggle
21. (6.1) Comes the Inquisitor
22. (6.2) The Fall of Night
Season Three ("Point of No Return")
1. (1.1) Matters of Honor
2. (1.2) Convictions
3. (1.3) A Day in the Strife
4. (1.4) Passing Through Gethsemane
5. (2.1) Voices of Authority (this was originally meant to air before
"Passing Through Gethsemane," but since the events of this
episode tie into the beginning of "Dust to Dust," and aren't
mentioned at all in "Gethsemane," the initial airing order
is actually an improvement)
6. (2.2) Dust to Dust
7. (2.3) Exogenesis
8. (2.4) Messages from Earth
9. (3.1) Point of No Return
10. (3.2) Severed Dreams
11. (3.3) Ceremonies of Light and Dark
12. (4.1) ** A Late Delivery From Avalon
13. (3.4) ** Sic Transit Vir
14. (4.2) Ship of Tears
15. (4.3) Interludes and Examinations
16. (5.2) ** Walkabout
17. (4.4) War Without End, Part One
18. (5.1) War Without End, Part Two
19. (5.3) Grey 17 Is Missing
20. (5.4) And the Rock Cried Out, No Hiding Place
21. (6.1) Shadow Dancing
22. (6.2) Z'ha'dum
Season Four ("No Surrender, No Retreat")
1. (1.1) The Hour of the Wolf
2. (1.2) Whatever Happened to Mr. Garibaldi?
3. (1.3) The Summoning
4. (1.4) Falling Toward Apotheosis
5. (2.1) The Long Night
6. (2.2) Into the Fire
7. (2.3) Epiphanies
8. (2.4) The Illusion of Truth
9. (M.3) ** Movie - Thirdspace
10. (3.1) Atonement
11. (3.2) Racing Mars
12. (3.3) Lines of Communication
13. (3.4) Conflicts of Interest
14. (4.1) Rumors, Bargains and Lies
15. (4.2) Moments of Transition
16. (4.3) No Surrender, No Retreat
17. (4.4) The Exercise of Vital Powers
18. (5.1) The Face of the Enemy
19. (5.2) Intersections in Real Time
20. (5.3) Between the Darkness and the Light
21. (5.4) Endgame
22. (6.1) Rising Star
23. (6.2) The Deconstruction of Falling Stars
Season Five
1. (1.1) No Compromises
2. (1.2) The Very Long Night of Londo Mollari
3. (1.3) The Paragon of Animals
4. (1.4) A View from the Gallery
5. (2.1) Learning Curve
6. (2.2) Strange Relations
7. (2.3) Secrets of the Soul
8. (3.1) ** In the Kingdom of the Blind
9. (3.2) A Tragedy of Telepaths
10. (3.3) Phoenix Rising
11. (3.4) The Ragged Edge
12. (2.4) Day of the Dead
13. (4.1) The Corps is Mother, The Corps is Father
14. (4.2) Meditations on the Abyss
15. (4.3) Darkness Ascending
16. (4.4) And All My Dreams, Torn Asunder
17. (5.1) Movements of Fire and Shadow
18. (5.2) The Fall of Centauri Prime
19. (5.3) Wheel of Fire
20. (5.4) Objects in Motion
21. (6.1) Objects at Rest
22. (M.4) ** Movie - River of Souls
23. (M.6) ** Movie - The Legend of the Rangers
24. (6.2) Sleeping in Light
Spinoffs
1. (M.5) Movie - A Call to Arms
2. Crusade - This ordering, which JMS specified, ignores the uniform change in favor of maintaining continuity of storyline.
1. (3.3) Racing the Night
2. (4.2) The Needs of Earth
3. (4.1) The Memory of War
4. (1.2) The Long Road
5. (4.3) Visitors from Down the Street
6. (1.3) The Well of Forever
7. (5.1) Each Night I Dream of Home
8. (2.2) Patterns of the Soul
9. (2.1) The Path of Sorrows
10. (2.3) Ruling from the Tomb
11. (3.1) The Rules of the Game
12. (1.1) War Zone
13. (3.2) Appearances and Other Deceits
# War Zone (108)
# The Long Road (107)
# Appearances and Other Deceits (113)
# The Memory of War (102)
# The Needs of Earth (101)
# Racing the Night (103)
# Visitors From Down the Street (104)
# Each Night I Dream of Home (105)
# The Path of Sorrows (109)
# Patterns of the Soul (110)
# Ruling From the Tomb (111)
# The Well of Forever (106)
# The Rules of the Game (112)