Season 2 and Earlier
For Reasons Not Worth Going Into - Pre-series, how Chuck came to Atlantis.
"A Momentary Lapse of Sanity" - Sometime post-Epiphany
"Salve ad Domum" - set the same day as "The Return, Part II"
Spiraling Towards Disaster - Lorne's POV
Botany Strikes Back - In which Parrish and Katie save the day.
"It's Character Forming" - a few weeks after "Reunion"
"First Time For Everything" - late season 3
"Evan Lorne's No Good, Very Bad Day" - late season 3
"A Few Short Outings"
Seven Regrets John Has About Love
Season Five (AU):
Into the Whirlwind - The Big One, where Atlantis separates from Earth.
Flashpoint - The aftermath of the above.
These take place at points during the two big fics:
PACMAN - Plotting ensues!
Recommended Stress Relief
The Apocrypha - aka "Stuff that got Jossed or is otherwise no longer part of the series, usually due to poor early writing skills."
"Take My Love
"To Seek Out New Life"
"And To Boldly Go(Strange New World Challenge)
"Five More Outings"
I Blame Your Parents - This story has since been Jossed multiple times, and then parts of it were scavenged for the Big Fic.