I found two decent DS9 videos on Youtube. One to Johnny Cash's "Hurt" (before anyone points it out I know it's a cover). The other with VNV Nation's "Endless Sky" that covered Sisko's journey as the Emissary.
I know the latter:
http://www.youtube.com/watch?v=5BU1E3xW4lE
but I really can't find the one set to Cash's "Hurt".
There is one set to Christina Aguilera's song called "Hurt"

lame song, but
nice video about Ziyal.
A few other DS9 videos I like include:
Garak: Obsidian Order Man
http://www.youtube.com/watch?v=qVV-8f1kOvE - very fun video
With or Without You (Odo/Kira)
http://www.youtube.com/watch?v=9hVB1kddPb0
This one is really great:
Gul Dukat: The End Has Come http://www.youtube.com/watch?v=ATVh1tqtI80 - the author has bravely incorporated the Pah-wraiths storyline... you might have already know from my 100 rants that I despise the storyline, but the video is pretty good and almost manages to make sense out of it.
The Pah-wraiths are still more suitable to make fun of, as in this funny video:
Ring of Fire Caves: http://www.youtube.com/watch?v=kiZ8xOLkZPo
Another one, by the same author, was even funnier:
Strange Bedfellows:
http://www.youtube.com/watch?v=_cDNIuWdSQg but unfortunately the music track ("Strangers in the Night" by Frank Sinatra) has been disabled by Youtube

Just play "Strangers in the Night" over it, and it becomes really hilarious - especially the line "
something in your eyes was so exciting..." (guess which scene that was set to...)
My favorite Star Trek fanvideo is
Make This Go On Forever -
http://www.youtube.com/watch?v=SfdPwvA9wIQ - about Spock from both realities, Prime and Alternate - with clips from ST09 as well as TOS and TWOK, set to the Snow Patrol song. (Make sure you read the description!)
Another really good one about Spock - this time about TUC and Spock/Valeris:
Hallelujah -
http://www.youtube.com/watch?v=6sl5Tv0JE2s
And I have to include the one about Spock and women (not just romance... women in general) set to Interpol.
Spock and the ladies http://www.youtube.com/watch?v=7o5Wezhzf9s
I used to have a bunch of great BSG videos in my Favorites, but most of them seemed to be taken down.

They included a Baltar video set to Muse "Mao of the Problematique", Helo video set to the same song (it is still on YT, but YT forced the author to change the song to something stupid), a Baltar/Six video set to "One Caress" by Depeche Mode, a Baltar video set to "The Great Below" by Nine Inch Nails, a Starbuck video with clips from "Maelstrom" set to "Give Me Strength" by Over the Rhine and another one with the same theme set to "Home" by Depeche Mode, two different Boomer/Chief videos set to "Missing" by Evanescence, a video about Baltar's trial set to "Walking In My Shoes" by Depeche Mode (which I gave the idea to my YT friend for, and he made a really good video... I haven't made any of my own yet, but I will)...
Here are a few that have survived:
Our Enemies, Ourselves http://www.youtube.com/watch?v=5qhcvpWelzI
Broken Toy (Saul Tigh/Ellen)
http://www.youtube.com/watch?v=EdL00gfbi6A
Battlestar Galactica and "dance with the devil" http://www.youtube.com/watch?v=oeGkqW3YvCE
Sleeping with Ghosts - Baltar/Six (and Placebo)
http://www.youtube.com/watch?v=QXSb-PwfyTs
The Guilt of Those Who Ran (basically Lee's speech at the trial, but well edited)
http://www.youtube.com/watch?v=AKqG5NOvAG8
other shows:
La Femme Nikita fanvideo:
Eden - Nikita and Madeline (NOT femslash!)
http://www.youtube.com/watch?v=0xDfbdXNc_I
Haunted (Xena/Ares) -
http://www.youtube.com/watch?v=geij_kWl1J8 - two guilty pleasures merged into one,
Xena the Warrior Princess and Evanescence
Heroes: Disarm (Sylar/Elle)
http://www.youtube.com/watch?v=oeWJnoy33SY
There was a really fun video about Sylar set to "In the Dark of the Night", but I can't find it anymore - I guess it has been taken down, too.
and... prepare yourself for the best video ever...
John Locke's Secret Mr Clean's commercial!! http://www.youtube.com/watch?v=UYFmHgaQMBI
here's the sequel!
http://www.youtube.com/watch?v=1BEEVbvcqp0
and the final one:
http://www.youtube.com/watch?v=Tv7wLvN4oT4