Gen

Dean is from Mars, Everyone Else Comes from Venus Dean knew there was something off about his father from the moment they entered the cabin. What he discovers is worse than he could have imagined.
Looking After Yourself  A baby on the doorstep is the least of the Winchester's problems.  
Heat and Dust (Angst warning!) John falls down a hole. Pain and humiliation follow.
Legal Advice (A comic in three panels.) The Winchester boy's first time in jail, in picspam fcomic form!
Aladdean  Alladdean wakes up trapped in a cave of wonders, with strange memories. Luckily, a genie with an awesome bitchface is around to help him out.
Grinding Bones to Make My Bread Giant!Dean. Featuring both crack and angst. Go me!
Haunted Joe Peterson's room is definitely haunted. He needs help. (Now friendslocked, since my entry to a RL writing competition is sort of based on it. Feel free to friend me if you're desperate to read *g*) 
When In Rome The Winchesters get zapped back to ancient Rome. Dean bitches about the clothes.
Alternate Universe Comics presents: Natural A comic strip about Sam and Dean Chevrolet, civilians. 
Mea Culpa (The Habeus Corpus remix) Remix of lemmealone's fic, in which Sam goes to confession while at Standford. Angsty. Written for spnremixfics.
Don't Know Your Claret From Your Beaujolais Sam is the demon Jesus. He has power. Crack occurs.

Bureaucracy 'verse

You know, the funny one in which Sam has taken charge of the demon army, saved his brother's soul and now finds himself the harassed lord of the world's first ever Independent Demon Republic. I class these as crack-lite, as in, crack, but with characters and emotions and stuff! All named after old movies, for no particular reason. Spoilers for 2.22.

(Posted in written order, which might make the most sense. Comment if you'd like a chronological order as well!)

The Odd Couple The one where Sam is busy, and Dean's annoying.
Some Like It Hot (Apparently) The one where Deanland is won, and Sam has a meeting.
Guess Who's Coming to Dinner? The one where Dean plays dress up, and Sam frets.
The Third Man The one where Sammy throws his first dinner party, and finds Dean a job.
Gone With The Wind The one where it's Dean's first day, and Sam frets some more.
The Outsider The one from an outsider's POV.
It's a Wonderful Life The one with lots of little scenes, prompted for my one month LJ anniversary.
Vertigo The one where Dean gets on a plane.
Bonnie and Clyde The one where Bobby and Ellen get drunk and prank the US government.

Also, ashlesha17 has written a story in this verse! I'm officially classifying hers as an AU, so, in alternative!Bureaucracy verse, there is: The Man That Would Be King 

Crossovers

Hearts, Ghosts and Jelly Babies (Dr Who and Supernatural)

Slash

The "It could totally have gone down like this" series. Complete! 
How The Demon might Have Been Defeated Ridiculous cracky AU. YED POV. (Acronyms, yay!)
What Might Have Happened After A continuation, featuring a wedding. Outsiders POV
What Could Have Hapened Next  Further adventures in crack. Ellen's POV. (Guest starring Bobby.)
How It All Could Have Ended Up  The boys tell their friends, and hold a wedding party. Bobby's POV

Hancuffed by Lust: The Radio Adaptation The title explains it all, really. A deeply serious mpreg masterpiece.