I really liked this deadzone cross too bad it's not longer(scroll down passed the recs)
The Club
http://valiant.livejournal.com/26808.html#cutid1

Quantum Leap cross
I haven't read this one because I keep forgetting about it. She has an amazing crossover with Medium(which you should check out too).
Leapin’ Lizards
http://gwendolyngrace.livejournal.com/68314.html


One of my favorite Sentinel crossovers
Twenty Four Hours
http://briarwood.livejournal.com/289308.html

Providence (http://www.fanfiction.net/s/9063470/1/Providence)
Criminal minds crossover

I've got a few!

Criminal Minds

Defect by Kikkimax - Dean is finally captured by the FBI just as his time runs out. Gen. Takes place in the SPN universe at the end of the second season and goes in a different direction than season three. http://www.fanfic.otherplaces.net/defect.htm (sequels: http://www.fanfic.otherplaces.net/hell.htm, http://www.fanfic.otherplaces.net/page80.html)
,
The Time Has Come to be Gone by Jujuberry136 - 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. http://jujuberry136.livejournal.com/48428.html (sequels: http://jujuberry136.livejournal.com/64499.html, http://jujuberry136.livejournal.com/95516.html)

This Bitter Life by art_savage - The Winchesters and the FBI's Behavioral Analysis Unit investigate the same case, a series of mysterious deaths on the grounds of a South Carolina plantation. http://art-savage.livejournal.com/21902.html

Sour Cherry Pie Life by faithburke - Dean has retired to the civilian life. Too bad no one told the serial killer currently stalking teenagers in Indiana.
http://faithburke.livejournal.com/50588.html

Mask of Sanity by reading1066 - (Part of the Strangers and Angels 'verse) Sam and Dean hear about a case that also brings the BAU to town. The hard part comes when they are spotted and the Winchesters try to keep their friends from being arrested as accessories. http://reading1066.livejournal.com/?skip=20&tag=mask%20of%20sanity

NCIS

Out for Blood by superbadgirl - Someone from Dean and Sam Winchester’s past comes back to haunt them…and while they're at it, they also haunt a member of the NCIS team. http://superbadgirl.livejournal.com/484586.html (sequel: http://superbadgirl.livejournal.com/1006916.html)

Of Hunters and Agents by rosedraquia - When Tony, Gibbs and Dean are trapped in an underground survival course by a serial killer, what will they do? Are the Agents willing to work with a known murderer in order to survive? And is everything truly as it seems? http://rosedraquia.livejournal.com/2075.html

Agents and Hunters by sg2009 - People who work in Abby's lab are never what they seem. And Sam is no exception. http://www.fanfiction.net/s/5385224/1/Agents-and-Hunters

Way to Kill by maras_morgue - Special Agent Jethro Gibbs knows how to solve crimes, but what happens when a meeting with a strange young man involved in an even more bizarre case aims to prove that maybe science can’t explain everything? http://sn-crossovers.livejournal.com/460404.html

Volatile Compounds by gekizetsu - The boys finally flash the wrong counterfeit badges while investigating murders on a Naval base. http://www.fanfiction.net/s/5199196/1/Volatile_Compounds

Encounters with the Enemy by legoline - They really thought they were done with being arrested at crime scenes. http://legoline.livejournal.com/873975.html

Merlin

Two Boys from Kansas in King Uther's Court by Ariadne's_string - http://ariadnes-string.livejournal.com/20479.html (sequel: http://ariadnes-string.livejournal.com/30137.html)

Men of Legend by hell's_half_acre - When a sorcerer summons monsters from another world, Merlin must summon heroes from another world to help save Camelot. Meanwhile, Dean and Sam Winchester didn't even know they were summon-able. http://hells-half-acre.livejournal.com/363167.html (check out the fabulous "demented 'verse" for HP crossovers)

Where Angels Tread by emmbrancsxx0 - When Sam gets trapped by the Weeping Angels in medieval Camelot, Dean employs the help of some strange new friends to get him back. Meanwhile, Sam and Merlin stumble upon a plot that may kill the king. (also includes Dr Who and Sherlock) http://archiveofourown.org/works/699909/chapters/1289394

Regarding Ways to Kill. I found it on FFN as complete. Here you go. (I'll need to fix it on delicious)
http://www.fanfiction.net/s/4281158/1/Way-To-Kill

Until You're Resting Here With Me (http://archiveofourown.org/works/368660/chapters/600153) by nyxocity

Accidentally trapped traveling through time through a project of his own design, Dr. Jensen Ackles finally finds himself twelve years in the past, in his own body, face to face with Jared Padalecki. His memory shot through with holes from time traveling, Jensen doesn't remember exactly what happened between them in the past, but he knows how he feels about Jared, and he knows things ended badly. Given a chance to do it right this time, can he change history—or does destiny have bigger plans?

One of the best x-overs I've ever read.

I'm working from my cell phone so I can't give you specifics but at sentinel fic find there are many links to sentinel supernatural Xovers

sentinelficfind.livejournal.com/tag/crossover%3A%20supernatural

Assume you've looked at the tags for the fandoms you're interested in, but the last time this was mentioned (I think) it was a WIP and it is now finished, so for NCIS

When Worlds Collide by elfinblue
http://www.fanfiction.net/s/9018850/1/When-Worlds-Collide

When you're looking for multiple shows, a good place to start (for quantity, at least) is FF dot net crossover page for Supernatural
http://www.fanfiction.net/crossovers/Supernatural/2237/


And the current round of Supernatural Cross Big Bang is posting now, and they have master lists and tags for you to hunt through

http://sncross-bigbang.livejournal.com/

And you didn't mention Numbers, but in case you're interested, here's a good one


Take a Long Line by Derry
Sam & Dean are after a firestarter in LA. The Numb3rs crew take a look at the Winchesters
http://www.fanfiction.net/s/3400565/1/Take_a_Long_Line

Not that I'm obsessing -
Another series you didn't mention but you implied you were open to others --

Smoke on the Water by ratherastory for claudiapriscus
Supernatural, Burn Notice
General AudiencesNo 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

Also, this link to a previous request (comments one and three) have some good Harry Potter crossovers -

http://spnstoryfinders.livejournal.com/7446616.html#comments

And concerning a rec made above, under NCIS, Way to Kill by maras_morgue - as far as I can tell it is WIP since 2008 and the author's journal is gone -- the links aren't internal to the story but I'm not sure I can post 11 active links -- so if you go to the crossover community listed in the post above [ http://sn-crossovers.livejournal.com ], hit the tag for NCIS and then go back 50 posts (5 pages) you'll be at the start of the story - she posted almost entirely in February and March of 2008 but stopped after part 11, although it was still marked tbc. If someone else knows differently, feel free to share.

And here's another place to look - an archive (supernaturally twisted) http://www.spntwisted.com/

http://www.fanfiction.net/s/4281158/1/Way-To-Kill

Complete! Thanks for pointing that out. I'll switch it over on my delicious link

awesome. Thanks!

I have a tag of crossovers on my recs page. it's almost exclusivly harry potter crossovers and Supernatural crossovers and i think they are all fairly long, so have a look!

whoops! forgot the link! http://aikawa-akihiko.livejournal.com/tag/crossover

Turn It Up To Eleven - MacGyver http://strangevisitor7.livejournal.com/78456.html

NCIS And The Haunted Computer http://tassosss.livejournal.com/50239.html

Five Times Dean & Tony Bumped Into Each Other - NCIS http://tassosss.livejournal.com/115648.html

1/Silent Healing - CSI-M http://sn-crossovers.livejournal.com/605700.html
2/Silent Hunter - CSI-M http://wincest.livejournal.com/1560925.html

A Loaded God Complex - Medium http://gwendolyngrace.livejournal.com/116171.html

The Ghost In The Lab - Bones http://like-a-raven.livejournal.com/3857.html

Righteous Man In A Shallow Grave - Bones http://bellatemple.livejournal.com/605615.html

There'll Be Peace When You Are Done - Merlin http://iseult-variante.livejournal.com/48868.html

It Could Grip It By The Husk - Merlin http://deirdre-c.livejournal.com/253010.html

BY ANY NAME I CALL YOU BELOVED - Merlin http://the-sparkhouse.livejournal.com/4762.html

Merlispn - Merlin http://onyxexistance.livejournal.com/107505.html

Unexplained - Numb3rs http://sn-crossovers.livejournal.com/747989.html

Northern Lights - X-Files http://spn-summergen.livejournal.com/65790.html

Eat It Twilight - Criminal Minds http://liliaeth.livejournal.com/343958.html

Fanning The Flames - Criminal Minds http://mandraco.livejournal.com/21960.html

Reflections - Criminal Minds http://faithburke.livejournal.com/85517.html

A Hole In You And Me (That Pulls Us Together) - Criminal Minds http://hunters-retreat.livejournal.com/443787.html

The Sky Is Folding Under You - Pretender http://sn-slash.livejournal.com/2765975.html

Don't Judge A Book - Simon & Simon http://superbadgirl.livejournal.com/773555.html

Due Supernatural - Due South http://queenklu.livejournal.com/193027.html

A Cage Full Of Heroes - Hogan's Heroes http://sarosefics.livejournal.com/29887.html

I hope some of these are what you're looking for.

Harry Potter/ Supernatural
If you haven't read Damned Demented Demons by HellsHalfAcre, it's one of the best fanfics I've read. And it's super long when you consider its multiple sequels and timestamps.
http://hells-half-acre.livejournal.com/190948.html

You people are AMAZING!!!!!!!! Thank You! for all the good links!