Pairing: Jennifer Keller/Ronon Dex are the main pairing for the overall series, but as the series continues we get other pairings introduced including the main secondary pairing: Laura Cadman/John Sheppard. Also Rodney McKay/Evan Lorne, Teyla Emmagen/Carson Beckett (clone!Beckett fyi) and some SG-1 ships in House of Cards (fourth fic) including: Samantha Carter/Jack O'Neill, Vala Mal Doran/Daniel Jackson and mentions of Carolyn Lam/Cameron Mitchell (and past McKay/Mitchell). Main page says all of this too.
Fic Title: Dark Places in the Soul Series
Author: Kiera Marcos
Link: http://keiramarcos.com/fan-fiction-index/stargate-atlantis-fan-fiction/dark-places-in-the-soul-series/ -- master list of fics
Rating/Warning(s): PG - NC-17
Genre: fork in the road, AU, series, violence, sexual situations, alien bonding rituals, action,
WIP?: series is incomplete but all the individual stories in it are complete
Why This Must Be Read: The series begins very much focused on the Ronon/Keller relationship, what it means to them, personally, professionally, and the first three fics of the series almost exclusively focus on this. As the series goes on, and it spans s4-5, it shows you it's also very much about Atlantis constant struggle against Michael, who is the main antagonist of the series. An interesting and frankly different take to most of the fic I've seen out the for Ronon/Keller this series becomes interesting as you delve deeper in Michael's plans and character's past. Full disclosure: some (purely personal) characterisation points aside this fic does a wonderful job with it's characters, their relationships with each other (romantic and otherwise), and plot.
Also, I'm including this one expert bc before I finished the last fic in the series I was all prepared to write Sam Carter/He Who Shall Not Be Named as a pairing, but then they just had to call him by name. Either way, even if you don't read the fic, this most cannot be missed.
Sam leaned forward and rested one chin on her hand. “I mean, you know if I wasn’t already uber involved with He Who Shall Not Be Named—you would have totally been on my list years ago.”
Rodney grinned. “You’re doing Lord Voldemort? Kinky.”