As the title suggests, I have made a guide to help people understand what is and isn't canon in the B5 universe. Feel free to provide any helpful suggestions which might improve this guide.
CANON IN THE B5 UNIVERSE
TELEVISION AND MOVIES:
This may be extremely obvious, but it's probably a good idea to list all visual works of B5 first. All five seasons of Babylon 5, along with the pilot movie "The Gathering" and TNT movies "In the Beginning", "Thirdspace", "The River of Souls" and "A Call to Arms", along with the recently released "The Lost Tales: Voices in the Dark", the failed pilot "Legend of the Rangers: To Live and Die in Starlight" and B5 spin-off series Crusade are all, of course, canon.
Availability: All Babylon 5 episodes (in season boxed sets), movies, and spin-offs listed above are available in most stores that sell DVDs, both retail and online.
Along with the various TV episodes and movies, there are other works of fiction which are part of B5 canon. Some people are confused as to whether certain books, comics, stories, and other works of literature are considered canon in the B5 universe but this guide should help people understand what should and should not be considered canon.
The first set of Babylon 5 novels to be released are a set of 9 novels from Dell Books. While all of the books in the series contain canonical elements from the series, only two books have been considered mostly or fully canon by JMS.
Book #7 "The Shadow Within" by Jeanne Cavelos is considered 90% canon. JMS hasn't yet stated what parts of the book are and aren't canon, but he has stated that the story of Anna Sheridan is completely canon. Other parts of the book deal with Sheridan on the Agamemnon and a plot by the Homeguard to destroy Babylon 5.
Book #9 "To Dream in the City of Sorrows" by Kathryn M. Drennen is considered 100% canon. The book is about Sinclair after he was reassigned to Minbar as well as the development of the Rangers. The story also involves what happened to Catherine Sakai and how Marcus Cole became a Ranger.
The next set of nine books came in the form of three trilogies, all of which are considered full canon. The trilogies are as follows:
Psi Corps Trilogy by J. Gregory Keyes:
Dark Genesis: The Birth of the Psi Corps
Deadly Relations: Bester Ascendant
Final Reckoning: The Fate of Bester
Legions of Fire Trilogy by Peter David:
The Long Night of Centauri Prime
Armies of Light and Dark
Out of the Darkness
The Passing of the Technomages Trilogy by Jeanne Cavelos:
The Psi Corps Trilogy deals with the origins of the Psi Corps as well as more backstory on Bester along with what happens to him after the end of the show. The Legions of Fire Trilogy tells the story of Londo and Vir on Centauri Prime after the end of the show. The Passing of the Technomages Trilogy tells the story of the Technomage Galen and how his story connects to the events of Babylon 5 and Crusade.
Availability: All books listed above should be in stock in most bookstores as well as online.
JMS, being a huge fan of comics, wrote and outlined several Babylon 5 comics, published by DC Comics.
The first issue "In the Darkness Find Me" was written completely by JMS, and the next three, "Treason", "In Harm's Way" and "The Price of Peace" were outlined by him.
The next four stories (5-8), all outlined by JMS created a story-arc called "Shadows Past and Present" and comprised of "With Friends Like These...", "Against the Odds", "Survival the Hard Way" and "Silent Enemies".
Issues 9 and 10 conflicted heavily with the series so are not generally considered to be canon. However #11 "The Psi Corps and You!" is considered to be canonical.
B5 comics had disappeared for a while but came back in issues #3-8 of the UK Babylon 5 Magazine. The comic series, called "In Valen's Name" taking place after the end of the Shadow War, was co-written and outlined by JMS and later on split into three issues in the U.S. These comics are, you guessed it, canon!
Some versions of The Lost Tales DVD (bought at Best Buy) included a 6-page mini-comic written by JMS paying tribute to two recently deceased lead actors on the show.
It has also been announced that as of 2006, JMS is finishing up the manuscript for a 100-page B5 graphic novel which is to be published by Wildstorm Productions. No other details have been given for the time being.
Availability: There is limited availability for all comics listed above. Most of the original comics as well as "In Valen's Name" can be bought used from private sellers on websites such as Amazon.com and eBay.com. The Lost Tales Tribute comic is only available for a limited-time on some Lost Tales DVDs, namely those bought at Best Buy.
After the show ended, JMS wrote a set of three short stories in the "Amazing Stories" magazine. "The Shadow of His Thoughts", another story about Londo after the end of the show, "Genius Loci", a story about G'Kar and Lyta's adventures after the series, and "Space, Time and the Incurable Romantic" which brings closure to the story of Marcus and Ivanova.
Another set of short stories were published in the Babylon 5 Magazine, all canon: "Hidden Agendas" by JMS, "True Seeker" by Fiona Avery, and "The Nautilus Coil" by J. Gregory keyes.
Now as we all know, Crusade was cancelled prematurely. The show was intended to have 22 episodes for the first season and some of the unproduced episodes already had partially written scripts. These scripts were released on Bookface.com for a time, the stories were: 1x14 "Value Judgments" by Fiona Avery which involved Telepath War criminal Alfred Bester, the next story was 1x15 "To the Ends of the Earth" by JMS about a Shadow-Hybrid vessel that Captain Gideon finds, and the last story, 1x22 "The End of the Line" also by JMS was intended to be the season finale.
I feel I should also mention that the novelizations of the B5 movies "In the Beginning", "Thirdspace", and "A Call to Arms" are also canon.
Aside from written/visual material, anything said by JMS himself is also considered 100% canon.
Availability: The short stories are extremely hard to find these days as the stories are only available in their original prints. While the Crusade scripts were available at one point, they were pulled because of illegal distribution of said scripts around the web. The novelizations should be available mostly anywhere.
I suppose that about does it, for now. I have comprised a list of what I think is probably the best order to watch/read the entire canon series. Not everything is in absolute chronological order, but I think this is probably the most enjoyable way to go through the series:
Season 2 up through "The Geometry of Shadows"
Original B5 Comics (1-8, 11)
The Rest of Season 2
The Shadow Within
To Dream in the City of Sorrows
Season 4 up through "Into the Fire"
In Valen’s Name (1-3)
The Next Two Episodes in Season 4
The rest of Season 4
In the Beginning
Season 5 up through "Objects at Rest"
Amazing Stories Short Stories (1-3)
B5 Magazine Short Stories (1-3)
The River of Souls
Legend of the Rangers: To Live and Die in Starlight
A Call to Arms
Unproduced Crusade Scripts
Psi Corps Trilogy
Legions of Fire Trilogy
The Passing of the Technomages Trilogy
The Lost Tales: Voices in the Dark
The Lost Tales Tribute Comic
Season 5 Finale "Sleeping in Light"
Like I already said, not everything is in chronological order but I have put everything in what is probably the most enjoyable order. "In the Beginning", can really be seen anytime after season 4 because while the bulk of the story is about the Earth-Minbari War, it was told through Londo over well into the future, so you can choose to watch it right after season 4 or anytime after that. If you are really worried about where events from the written/ilustrated works fit into the series, then you should go to this website for accurate information on when all events from the canon B5 universe takes place.