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.