I have two self-recs:
Salt and Blood (http://emebalia.livejournal.com/22793.html)
Summary: That serial killer who blew himself up down in Florida? Still active. So either they got the wrong guy or we've a ghost-problem; Dexter/SPN

Even Monsters have a Social (http://emebalia.livejournal.com/59765.html)
Summary: When two supposed to be dead mass murderers cross path with their latest number the case seems pretty clear to John. Person of Interest/SPN

Some of my favorite crossovers. I hope you find something you like.

Numb3rs/SPN crossover,

Title: The Production and Decay of Strange Particles Sam/Dean, Charlie/Don

Pushing Daisies/SPN

Baking For the Dead

Dean and the Piemaker Gen


The ConMand and the Pieman Gen

Boondock Saints/SPN
A St. Patrick's Day to Remember Gen

I have a quick and a not so quick version of this...
one is my own crossover, SPN/LieToMe which you find here: The Truth Lies Beneath (http://archiveofourown.org/works/439132)

And I'll just point you towards sn_crossovers, a whole community catering to your specific needs. Of course they also host links to my favourite crossovers (mainly with Criminal minds) like 'Defect' for example. Enjoy!

I really enjoyed The Winning Scenario (http://virtualpersonal.livejournal.com/241801.html) and Dragon Spell (http://archiveofourown.org/works/3181757/chapters/6913142) by virtualpersonal, both of which are Sam/Dean (though I think they're unrelated in the first story?) and heavy on the Sam-whump. The first is a battlestar galactica crossover, and the second is dragon riders of pern.

Also, The Hunter Games (http://archiveofourown.org/works/519567/chapters/918082), which isn't so much a crossover as it is Sam and Dean playing the parts of Katniss and Peeta.

Men of Legend (http://archiveofourown.org/works/748772/chapters/1396965) is a really great gen spn/merlin crossover, and I loved astolat's Old Country (http://archiveofourown.org/works/164479) (Sam and Dean go to Hogwarts).

All these are gen.
SPN/NCIS
When Worlds Collide (https://www.fanfiction.net/s/9018850/1/) One of the best crossovers I've read.
When a kidnapped Tony DiNozzo is rescued by legendary - and supposedly dead - serial killers Dean and Sam Winchester, the NCIS team takes over the Winchester investigation. What they find is a file filled with contradictions and impossibilities.
NCIS and the Haunted Computer (http://tassosss.livejournal.com/50239.html#cutid1)
The computer did it.

SPN/Criminal Minds
The Time has Come (http://jujuberry136.livejournal.com/tag/timehascomeseries) A trilogy of crossovers, all linked here. The first fic is at the bottom of the page.
' When Aaron Hotchner stepped into the interrogation room to interview one of the FBI’s most wanted unexpectedly apprehended earlier in the afternoon, he never thought the evening would end with bloodshed and rock references.'

SPN/Buffy the Vampire Slayer
Twisting the Hellmouth crossovers with Supernatural (http://www.tthfanfic.org/Category-1-30/Supernatural.htm). Twisting the Hellmouth is a website dedicated to Buffy crossovers. This link will take you to all those featuring Supernatural.

SPN/SG-1
The Syndicated Sci-Fi show (http://claudiapriscus.livejournal.com/18810.html)
A 'changing channels' fic. Sam and Dean have been lurching from show to show for days. They've been injured, humiliated, screwed with, and forced to live really bad writing. When they're finally plunked down in something a little calmer, if a little odd, they dare to hope they're being allowed a breather episode. After all, it seems to be a show about an expedition poking around some completely non-ominous ruins- like a fantasy version of a history channel special, the boys are sure it's bound to be nice and boring.

Happy Reading. I think I'm going to do some re-reading tonight.

My absolute favourite SPN crossover fic is a short oneshot that to this day never fails to take my breath away, for it leads to so many possibilities and what ifs for a show that I adore. Plus, it's my two favourite leads - together! :D

San Francisco (http://www.wraithbait.com/viewstory.php?sid=10393) - by Kris (NC17)
Summary: A chance meeting will change John Sheppards future...and Dean Winchester's as well.

Flip Side (http://archiveofourown.org/works/305558) - by skieswideopen (NC17)
Summary: Dean heads to Republic, Washington to hunt down a trio of monsters whose young victims all appear to have died of old age.
A/N: Set after season five of SGA and during season seven of SPN, but with only a few spoilers for either.

And one self rec...
Switch (http://archiveofourown.org/works/893580) (PG)
Summary: Dean mistakes black for navy.

Crossovers are my weakness too! I hope you found a number at my Delicious that you liked.

You've got loads of great recs already, so I'm just going to add two of my favourites on here:

Sam, Son of Adam (http://maychorian.livejournal.com/30950.html) - maychorian
"I don't…I'm not…no throne, no," Sam protested. His voice sounded utterly weak to his own ears, though, and so very easy to ignore. "I just want my brother." [Narnia crossover. Starts off with cracky undertones, but then things get intense.]

Take a Long Line (https://www.fanfiction.net/s/3400565/1/Take-a-Long-Line) - Derry
Winchester isn't stupid. Dangerous, unpredictable and often reckless. But definitely not stupid. So there has to be a good reason that, knowing full well that he's on the FBI's radar, Dean Winchester brazenly walked into a Federal Building. --[Numb3rs crossover. Really great outsider-POV of the dynamic between the brothers.]

I have read two excellent SPN/Pacific Rim crossovers:

Cardinal Hunter (http://zuben-fic.livejournal.com/81385.html)
Saving people. Hunting kaiju. The family business. [Sam/Jess, Sam/Dean]

Lemon Trees on Mercury (http://archiveofourown.org/works/887833/chapters/1711858)
Dean asks how the Jaegers work.
"Pilots," Dad says. "Pair for each unit."
Sam never had a chance at normal.
[Sam/Dean, Castiel/Meg]

X-men/SPN
Wolverines, Wendigos and Winchesters by Scifinuttx on fanfiction.net

Dark Angel/SPN
The Wellspring by Vegakrist on fanfiction.net

Just started a Harry Potter Crossover that you might be interested in - Wizards, Werewolves and Hunters, Oh My! (http://archiveofourown.org/works/3476096/chapters/7631696)

Dean's life is complicated. It turns out he's a wizard and Dad has insisted that if he has to have a magic son then at the very least his magic son is going to the best damn magic school there is... that speaks English. So now he's got to survive magic school, homesickness and the murdering psychopath after one of his friends - that weird dark haired kid with the scar and the glasses in the year below him (you might of heard of him). Not only that but there is still Sammy and the Family Business to contend with.

Surely magic will make things easier?

Smoke on the Water by ratherastory xovr BN. for claudiapriscus
Supernatural, Burn Notice
General AudiencesNo Archive Warnings ApplyGenComplete Work1 Sep 2010
TagsNo Archive Warnings Apply, Dean Winchester & Sam Winchester, Sam Axe & Fiona Glenanne & Michael Westen, Dean Winchester, Sam Winchester, Michael Westen, Sam Axe, Fiona Glenanne, Madeline Westen, Crossover, Community: spn_summergen, Case Fic, Hurt/Comfort,
SummaryCasefic. Former spy Michael Westen has enough problems of his own ―not least of which is figuring out who burned him and why. Now, on top of that, his mother is accepting jobs on his behalf. He really doesn't have time for this, but when he starts investigating the unsolved deaths of young people in Miami, he finds himself crossing paths with an unlikely pair of brothers. In Michael's line of work, suspicion is par for the course, and he has to figure out whether Sam and Dean Winchester are friends or foes before even more lives are lost.
Smoke on the Water by ratherastory xovr BN. for claudiapriscus
Supernatural, Burn Notice
General Audiences No Archive Warnings ApplyGenComplete Work1 Sep 2010

http://archiveofourown.org/works/210038
http://www.fanfiction.net/s/6293145/1/Smoke_on_the_Water as mousme id: 6293145

Bobby Singer Chronicles Hostile Territory xover aliens
The Bobby Singer Chronicles: Hostile Territory
http://dolimir-k.livejournal.com/956383.html
http://archiveofourown.org/works/210916
Author(s): dolimir_k
Artist: desree_rd
Crossover: Aliens

Sorry, should have specified -- AU wee:chesters

Shadow (https://www.fanfiction.net/s/5163432/1/Shadow) by Black-Raven3
Supernatural/Hellsing
Preseries
Summary: Sam remembers a recent hunt. Two weeks spent in Mt. Rushmore being hunted by shadows and a man in a red coat. The only hunt to ever truly get to his dad.

Edited 2015-03-09 03:28 am (UTC)

My favorite SPN cross-overs are written by khaleesian and crossed with The Fast & The Furious series. She wrote three.

Recharging which is gen with hints of Brian/Dom pre-slash-
http://archiveofourown.org/works/177882

Vaughn, New Mexico-
http://archiveofourown.org/works/177934

and its sequel: Valentine, Arizona, Night-
http://archiveofourown.org/works/177945

which are both Brian/Dom.