These are a few of my favorites!

Ascended Rodney
Ascending Order by Argosy
http://argosy.livejournal.com/61002.html

View Points by lavvyan
http://lavvyan.livejournal.com/99954.html

Aliens made'em do it!
Decisions by darkhavens
Four potions, four people...John's decision.
http://darkhavens.livejournal.com/123445.html

Showing by Chelle
John and Rodney are invited to be the honored guests of a newly crowned queen. They don't realize it includes spending a night of really, gloriously hot sex in an attempt to help her conceive.
http://chellefic.livejournal.com/3093.html

Amnesia
A Royal Deception by mandragora1
Rodney is made prince of a kingdom and has the memory of his life on Atlantis completely wiped. It’s John and team to the rescue.
http://community.livejournal.com/sga_flashfic/159098.html?style=mine

Broaden into Boundless Day by thingswithwings
Rodney forgets, Rodney assumes, John lets him...
http://thingswithwings.livejournal.com/17065.html

Lapse of Memory by The Huntress
John forgets about Atlantis and his relationship with Rodney. My heatbreaks a little for Rodney in this one.
http://www.area52hkh.net/ash/huntress/lapsemem.php

Rewind, Reboot, Restory by rheanna27
Rodney forgets and reverts to his asshole, pre-Atlantis self...John has a hard time dealing this Rodney on his original settings.
http://rheanna27.livejournal.com/83983.html

AU Atlantis

Team as Teens on Altantis
The Call by kitt
The gang go to school together on Atlantis
http://community.livejournal.com/sgastoryfinders/1875994.html#cutid1

Mensa AU
The Other Road by seekergeek
Fantastic Mensa fic! A must read.
http://seekergeek.livejournal.com/75801.html

Merman Rodney!
Through the Noise to the Sea by Sardonicsmiley
http://sardonicsmiley.livejournal.com/87157.html

Rodney a Science fiction writer, while Atlantis is real and writes about it unwittingly
The Long Journey Home by skoosiepants
http://skoosiepants.livejournal.com/178151.html?style=mine

Banal AU
All Great, though!

Business Competitors
Wokin’ Men (Somewhere To Go) by oneechan19
http://community.livejournal.com/nolonger19/8547.html

Clothing Designer
The Clothes Make the Man by Orithain and Rina
http://www.wraithbait.com/viewstory.php?sid=6842&warning=12
 
College Professors &/or Grad Student
Academic by rageprufrock
http://glitterati.talkoncorners.net/fiction/academic.php

Bell Curve series by rageprufrock
Professor McKay & Stripper/Grad Student John!
http://glitterati.talkoncorners.net/fiction/bellcurve/bellcurve.php

Stress relief by velocitygrass
http://velocitygrass.livejournal.com/68256.html#cutid1

The Theory of Acquired Characters by toomuchplor
Rodney poses as a grad student to lure Professor Sheppard to the Stargate Atlantis program
http://toomuchplor.livejournal.com/47420.html?style=mine

Cowboys
The Road to Nowhere by Le_Mot_Mo
Awesome AU!
http://le-mot-mo.livejournal.com/123600.html

Dog Walker
Walk this Way and its sequels by Yin 
http://yin-again.com

Detective John/CSI Rodney
Wrapped in a Red Ribbon by auburnnothenna
http://community.livejournal.com/sga_santa/79068.html

Fairy John
Fair by minnow1212
http://community.livejournal.com/undermistletoe/48389.html

Federal Agent
Hide and Seek series by rageprufrock
This story is greatness!
http://glitterati.talkoncorners.net/fiction/hindsight.php

Going for Gold!
Vancouver, British Columbia, Canada (2010) by sardonicsmiley
http://sardonicsmiley.livejournal.com/46746.html

Keep crossing paths since childhood
Intersections by Never
http://www.wraithbait.com/viewstory.php?sid=7062&textsize=1&chapter=1

Lake House Remix
Everything but Love by cottontail
http://cottontail.livejournal.com/134833.html

Let's get Married...But we're not involved!
Sting of Destiny by Jade_Dragoness
Dr. Rodney McKay needs to get married in a hurry to continue working in the states.
http://community.livejournal.com/sga_flashfic/170332.html

Meet on a cross town train!
Strangers on a Six Train by eye_queue
Ooooo! I love this fic so much. One of my all-time favorites!
http://eye-queue.livejournal.com/680.html

Politician
As wide as the Sky by seperis
http://soulcake.skeeter63.org/johnandrodney1.html

Regency Era Fic
A Regency SGA Tale by GraceandFire
John Sheppard is determined to bring to ruin the villainous McKay family. But young (ok, youngish) Rodney interferes with his plans.
http://www.wraithbait.com/viewstory.php?sid=5261

A Dangerous Desire or McKay Makes a Match by Janne_d
Awesome story! Check it out.
http://janne-d.livejournal.com/32547.html

Robot John!
The Soul and the Company Store Remix by Leah and Springwoof
http://leahwoof.livejournal.com/9838.html?style=mine
 
Shop Owner
A Place OnThe Corner by almostnever
John owns a bakery, Rodney loves the double chocolate muffins. An absolute FAVORITE of mine!!!
http://community.livejournal.com/mcshep_match/53637.html

A Supermarket in California by taffetablue
John courts Rodney with goodies from his supermarket.
http://taffetablue.livejournal.com/10542.html

Fair Trade by esteefee
http://esteefee.livejournal.com/12350.html

Teenage Rodney/John fic
The Best Things in Life are Free by smittywing
Remix of the film ‘Can’t Buy Me Love’ but sweetly done that its more entertaining than the film.
http://www.offpanel.net/smittywing/stories/tbtilaf.html

Stars of Track and Field by unamaga
http://unamaga.livejournal.com/207366.html

Widowed with a Kid
On Life and Living by WesleysGirl
Elizabeth gave John simple instructions on how to raise their girl after her death, but can he learn to live and love again. 
http://home.comcast.net/~wesleysgirl/fanfiction/sga

The Neighborly Detective and the Tragic Woobie Widower by Elayna
Rodney is widowed with a son, and John is a detective who just moved in next door.
http://furholt.net/elaynas_den/_McShep_Woobie.htm

Bad Sex
Or Actually really great, bad sex!
Do Over by Crysothemis
http://crysothemis.livejournal.com/74062.html

BDSM
Harmonic Function by Shaenie
Not usually my thing, but boy is it really good.
http://shaenie.livejournal.com/322545.html

Charm school for Rodney
Charmed by MrsHamill
John gives Rodney lessons on to how make friends and attract women
http://www.hawksong.com/~thammill/SGA_Fic/charmed.htm

Christmas Fic!
Tidings of Comfort and Joy by Tira Nog
http://tiranog.southroad.com/SGA/Tidings_of_Comfort_and_Joy.htm

Cute Little Ficlet
Taken by sheafrotherodon
Rodney kidnapped and a tad out of it.
http://community.livejournal.com/mcsmooch/21713.html

De-aged John
The Wisdom of Children by JenniferLupin
http://jlupinfic.livejournal.com/19648.html

Dexter-like John
John by Kho
http://kho.cruel-kindness.net/words/sga/john.php

First We’re Parents…Then comes Love
A Beautiful Lifetime Event by astolat
http://www.intimations.org/fanfic/stargate/lifetime_event.html

Supersymmetry by Lallybroch
“It's like talking to a miniature Rodney with a Colonel Sheppard filter. It's bloody disconcerting!”“It's like talking to a miniature Rodney with a Colonel Sheppard filter. It's bloody disconcerting!”
http://lallybroch.livejournal.com/30336.html

The Price that Life Exacts by Cathalin
John disappears for a year, but a baby is found who looks like him and has his dog-tags around her neck.
http://sgabigbang.talkoncorners.net/?view=fic&id=38

Future Fic!
Freedom's just another word for nothing left to lose by synecodochic
F**king Awesome, heartbreaking story! Words cannot express how much this fic should be read.
http://www.kekkai.org/synecdochic/sga/freedoms_just_another_word.html

Genderswap
Utterly HOT genderswap!
Stand-In by lamardeuse
http://lamardeuse.dreamhost.com/sg/standin.html

Rodney a Girl to begin with ...
Waging Romance on Meredith McKay & The Effects of Foreign Policy on the Domestic Agenda by sardonicsmiley
http://smiley.zonezine.net/html/92778.html
http://smiley.zonezine.net/html/95912.html

Hi Jeannie!
Mer and the Colonel by chocolatephysicist
Summary: Rodney McKay can’t lie. He really can’t. He’s lost entire fortunes playing poker because he can’t keep from giving himself away. So when he lies and tells his sister that he and John Sheppard are involved--he and the very straight John Sheppard--you know things are going to go terribly, horribly wrong.
I love, love this fic!
http://iloveatlantis.livejournal.com/73988.html

You’re My Wonderwall by ionaonie
Summary: John and Jeannie talk about some of Jeannie’s assumptions when she and Rodney were kidnapped by Wallace.
http://ionaonie.livejournal.com/118516.html

Hilariousness
Bang by rageprufrock
http://glitterati.talkoncorners.net/fiction/bang.php

Hookerfic John
King of Wishful Thinking by margarks
http://margarks.livejournal.com/tag/king+of+wishful+thinking

Misinterpretation by velocitygrass
After returning from Atlantis, John dates and gets $$$, Rodney makes a date and gives cash!
http://community.livejournal.com/mckay_sheppard/1827778.html?view=15717826#t15717826

I can't Believe you Love me! 
Resilience by Tira Nog
http://tiranog.southroad.com/SGA/Resilience.htm

Let’s Get Married! ...But we’re not involved!
Catch-19 by mmmchelle
I absolutely LOVE this marriage of convenience fic!
http://community.livejournal.com/mcshep_match/7221.html

A Not-So-Modest Proposal by reccea
http://reccea.livejournal.com/174188.html?style=mine

Rules of Engagement by velocitygrass
After the team returns to Earth, Rodney wants a job... his would-be employers don't like his reputation and someone suggest he gets married to make him a more suitable candidate.
http://velocitygrass.livejournal.com/62709.html

Mac-daddy Rodney, John wants some
Notching the Bedpost by Lenore
http://scribblinlenore.livejournal.com/285576.html

The Conversation by Lady Ra
An absolute must read!
http://www.visionsofprettyboys.com/Atlantis/TheConversation.htm

Mail Order Bride
No Refunds or Exchanges by astolat
http://community.livejournal.com/sga_flashfic/151595.html?style=mine

Matchmaker, matchmaker, make me a match!
eHarmony by tigerlady
Harmony wants to reward Rodney with a gift.
http://shetiger.livejournal.com/454303.html

Marines to the Rescue!
fic???maybe by helenish and crimsonclad
http://crimsonclad.livejournal.com/102936.html

Met once, then meet again years later
Second chances by z_rayne
 http://community.livejournal.com/sga_flashfic/172811.html?style=mine

Quantum Universe Interaction
Perfect Strangers Series by Madison
Fantastic series, highly recommended.
http://www.area52hkh.net/asm/madison/perfec01.php

Past Lives resurface
Total Recall series by ca_pierson and darkmoore
 http://community.livejournal.com/piersonfanfic/9115.html

Please don’t Let me be mistunderstood
Oblivious by astolat
http://www.intimations.org/fanfic/stargate/Oblivious.html

Rodney’s put in Charge of Atlantis
Repercussions by crazy_obsessed
John is held hostage by Kolya and Elizabeth refuses to rescue him.
http://crazy-obsessed.livejournal.com/9248.html

Transcendental by astolat
Absolutely love this fic!!!!
http://www.intimations.org/fanfic/stargate/transcendental.html

Rodney seeks his Soulmate, or a way to get this damn thing off!!!
"Happily Ever After" by cupidsbow
http://cupidsbow.livejournal.com/285366.html

Romance by the Shooting Range
Care in the holding by laceymcbain
http://www.stickymanpress.mediawood.net/careintheholding.html

Sentinel X-Over
Imperfections by Dasha
Rodney is a fragile Sentinel and John is assigned his guide.
http://soulcake.skeeter63.org/johnandrodney1.html

The Gathering by Keira Marcos
From The Sentinels of Atlantis series
Summary: Sentinel John Sheppard thought he’d spend his life unbonded and then he met Dr. Rodney McKay.
http://keiramarcos.com/2008/08/28/the-gathering-part-one/

Sex or Die!
Tango by astolat
http://community.livejournal.com/undermistletoe/31192.html?style=mine

Sex! Sure, but I’m Not Gay…just so we’re clear
Kid A by Speranza
Great, great story about having the slow realization that you’re in a relationship with someone you never expected and constantly fighting the urge not to freak out about it.
http://trickster.org/speranza/cesper/KidA.html

Slavefic John!
Advantage by resonant8
http://trickster.org/res/advantage.html

Sleeping Beauty, SGA style
Sleeping Atlantis by scribblinlenore
http://scribblinlenore.wordpress.com/home/stargate-atlantis/sleeping-atlantis/

Stuck alone with no one else but you!
Time in a Bottle by astolat
Stranded in a VR world together.
http://www.intimations.org/fanfic/stargate/time_in_a_bottle.html

Pallalax by Sajinn
Strangled in a different dimension together
http://sajinn.com/sgafic/parallax.html

Two Heads are better than One…or are they?
Double Occupancy by Isis
http://hieroglyfics.net/double.htm

Vacation on Earth
Ordinary Life by astolat and cesperanza
Kick ass action and an extraordinary H.O.T. John Sheppard
http://trickster.org/speranza/cesper/ordinarylife.html

We’re involved? Oh, so how come I didn’t know?
Touch by astolat
http://intimations.org/fanfic/stargate/Touch.html

An Inaccurate Telling by chelle and thegrrrl2002
Rodney gets jealous and lets someone think John and he are an idea.
http://chellefic.livejournal.com/5708.html

While John pines for Rodney, Rodney thinks of a mutually beneficial arrangement
Every Day in Every Way by velocitygrass
http://sgabigbang.talkoncorners.net/?view=fic&id=8

…another John pines for Rodney fic
Loves Me Not by astolat
http://intimations.org/fanfic/stargate/Loves%20Me%20Not.html

Where Rodney secretly pines for John fic
Screensaver by Danceswithgary
http://danceswithgary.livejournal.com/278413.html

Gen or Inexplicit McShep

Kick-ass Rodney fic
Rescue by tigs
Rodney walks into a bar to rescue the team from leather wearing, hairy deviants.
http://community.livejournal.com/sga_flashfic/397137.html

The Real Superman by  Tazmy
http://www.fanfiction.net/s/3047720/1/The_Real_Superman

X-Over with Gilmore Girls
Physics of the Spin by Mhalachai (WIP)
This is a really great take on the type of child McKay could produce…I just really hope Mhalachai throws in a little McShep in the near future, and I’ll be a happy camper.
http://www.tthfanfic.org/Story-15147/Mhalachai+Physics+of+the+Spin.htm