The old timelines are extremely expansive and confusing. Plus, they are not "canon" to me any longer, especially since they were largely written while the show was running and therefore do not cover all of show canon and contradict it in places. My current timeline, which I began in 2009, is now the only one I consider "canon." Hence, it will be much easier to list what's in the new timeline and who's the focus of each! I will try to list them chronologically, albeit this doesn't mean I wrote them in the order they take place. The Pendulum Swings was written first, but later I did some other short stories that I consider canon to this timeline and that come first. And occasionally, an old timeline story will still fit the new timeline and will be included.
And Then There Were Five (The Big 5, Noa)
The Worst Thing (Bakura)
A New Kind of Summer (Duke and David)
Someone Else to Come and Save Me (Duke and David)
Lost Souls Live Not Forever (The von Schroeders)
Chained to Despair (Yami/Thief King Bakura)
The Forgotten (Yugi, Atem, Yami/Thief King Bakura)
The Open Door (Atem and Yami/Thief King Bakura)
The Pendulum Swings (Bakura and Yami Bakura)
Adventures in Thief-Sitting (Bakura and Yami Bakura)
Waiting for a New Day (The bikers)
White is in the Winter Night (Bakura and Yami Bakura)
Never Felt So Empty (The bikers)
Silent Night (Bakura)
Taming the Darkness (Bakura and Yami Bakura and Yami Marik)
The next story should be Burning Starfire, but it is not. Why? Well, mainly because for a variety of reasons, I stalled on it and I'm not sure I ever will be able to revive it and write it to its conclusion. So for now, it is not considered part of the official timeline, and I may take some components from it and use them in other stories instead.
A Little Bit of Loneliness, A Little Bit of Disregard (Pete Coppermine from Yu-Gi-Oh! R)
Lead Me Through the Fire (Duke and David)
Commiseration (Duke)
Reasons of Existence (Duke and Snakes Tolliver)
Close Your Eyes, Clear Your Heart (Duke, David, Serenity, and Snakes Tolliver)
The latter three of these are included largely because they have the majority of my Duke and David character development. However, a couple of things in them are not canon to the timeline, making it a little bit awkward if you can't squint and just ignore them! For one thing, the characters are slightly aged up in those stories and I no longer want them aged up because I still want to have high school adventures go on. And also, Duke and David are not fully aware of Yami Bakura being back yet, but in the current timeline, they would be aware of it.
Every Side of Me (ensemble)
This one I'm a little unsure of, mainly because it's partially a tongue-in-cheek crossover with Pokemon and I'm not sure how well that works as part of my current timeline. However, it references events of several major stories in the timeline and there's nothing to say it couldn't be part of it.
Dragons at Dawn (ensemble)
An Eye for an Eye (ensemble, but emphasizing Marik, Yami Bakura, Atem, Bakura, Yugi)
It Happened on Maple Street (Bakura and Yami Bakura)
Someone Who Cares (Bakura and Yami Bakura)
Soul Release (Bakura and Yami Bakura and Yami Marik)
Shadow of the Night (Bakura and Yami Bakura)
Until You Find the Answers (Siegfried, Pegasus, Dartz, Seto, with other characters in supporting roles)
Static Code Analysis (ensemble, but focusing on Yami Bakura, Bakura, Seto, Mai, and the Big 5)
My Past is Not Today (Mai, Yami Bakura, Bakura, Joey)
Too Much That Time Cannot Erase (Mokuba, Seto, the Big 5, Yami Bakura, Bakura)
What is Justice? (Tristan, Yami Bakura)
True Night (Yami Bakura, Bakura, Tristan, Yugi, Joey, Tea, Yami Marik)
Tired of the Way That Things Have Been (Lector/the Big 5, Seto, Yami Bakura, Tea, Bakura, Mokuba)
A Christmas to Remember (The Big 5, Yami Bakura, Bakura, Seto, Mokuba)
Obsession in New Orleans (The Big 5, Seto, Mokuba)
Darkest Before the Dawn (The Big 5, Mokuba, Seto)
Among the Ashes (ensemble, emphasizing Yami Bakura, Bakura, the Big 5, Yugi, Duke, Seto, Mokuba)
Return to New Orleans (ensemble, emphasizing the Big 5, Seto, Atem)
Old Enemies, New Friends (ensemble, emphasizing the Big 5, Seto, Mokuba, Tea, Lumis, Umbra)
Forgive My Ugly Heart (The Big 5, especially Nesbitt and Lector)
Little Broken Heart (The Big 5, Mokuba, Seto, Noa)
Tears of a Human (The Big 5, especially Nesbitt and Lector)
I Won't Let You Pull Me Down (The Big 5)
The above story is very dark, and part of me is hesitant to say it really happens in the main timeline. The other part says it does, especially since nothing contradicts the main timeline and it has a great deal of protectiveness and Team as Family elements with the Big 5 that I would like to consider canon.
Walking With a Ghost (ensemble, focusing on the Big 5, Mako Tsunami, Duke, David, Serenity)
Mind Screw (The Big 5)
The Life and Times of the Purple Avenger (ensemble, focusing on The Big 5, Duke, Tristan)
Our Place in Time (ensemble, focusing on the Big 5 and Mokuba)
Light the Sky with Silver (The Big 5, Mokuba, Seto)
Fade Into the Rising Sun (Seto, Joey, Mokuba, The Big 5, Tea, Vivian Wong)
Falling Out of Time (The Big 5, Mokuba, Noa, Yugi, Lumis, Umbra, Vivian Wong)
Stirring Up Ghosts (The Big 5, Mokuba)
A Thousand Knives (Lumis, Arkana, Umbra)
You Can't Escape the Truth (Duke, Serenity, Tristan, David, The Big 5)
The End of All Things (ensemble, focusing on Yami Bakura, The Big 5, Lumis, Umbra, Seeker, Vivian Wong, Yami Marik, Zorc)
When All the Shades Are Gone (The Big 5, the bikers, Mokuba)
Rise With the Break of Dawn (Siegfried, Leonhard, Seto, Mokuba, The Big 5, Duke, Lumis, Umbra)
A Little Good News (The Big 5)
True North (ensemble, focusing on The Big 5 and Noa)
Cut Too Deep (cross with 5Ds, focusing on Kalin Kessler, The Big 5, Mokuba Kaiba, Seto Kaiba, Yugi Muto)
Christmas, Caroling, and Scary Ghost Stories (ensemble, focusing on Duke, Serenity, David, The Big 5, Melody/Miho)
One Ring to Rule Them All? (ensemble, focusing on Siegfried von Schroeder, Radley Ramon from 5Ds, and The Big Five)
And In the Darkness Bind Them (cross with 5Ds, focusing on Kalin Kessler, Radley Ramon, The Big Five, Solomon, Yami Marik, Lawton, Yusei Fudo, Antinomy)
Twilight of a Friend (Tea Gardner, Seto Kaiba, taking place during And in the Darkness Bind Them)
Sunrise of a Friend (Tea Gardner, Seto Kaiba, Mokuba Kaiba, with appearances from Radley Ramon and Kalin Kessler)
The Evolution of Dreams (takes place slightly in the future, focusing on Tea Gardner and Seto Kaiba)
Deja Vu (Joey Wheeler, Mai Valentine, takes place during the Dark Signer arc of 5Ds)
This list will be updated any time a new fic pertaining to the timeline is written. And also, if I think of any existing fics that apply. Every now and then I will write something that isn't part of the timeline because I wanted to test out the idea, such as Shards of Me. And then sometimes, events of really old stories will be referenced in the new timeline, such as Oreo's arrival, but with the unspoken implication that the old stories are not considered canon, only another version of some of the events within them. Yami Bakura of Frantic in Frisco is not the same Yami Bakura as in the new timeline; hence, despite Oreo's arrival sounding similar, it apparently happened on a different adventure in the new timeline.
The only place to find every fic in the timeline is at http://www.fanfiction.net/~Luckyladybug Occasionally I will post another copy of a story somewhere like Livejournal or Archive of Our Own, but neither location has everything. The old timeline stories are still available too. While I really prefer my more canon-accurate timeline and think it's written far better, I certainly have a fondness for those old stories and I'm very touched and moved that some people still like them!