God's Gonna Cut You Down by kiki_miserychic. -- Johnny Cash (remixed) + John Winchester = a match made in heaven. I especially love the slightly experimental nature of this one. *Not* just your average slapped-together footage vid but one with a lot of thought and creativity.
BUT THIS ONE might be my favorite: "If I only could/make a deal with God/and get him to swap our places," Placebo's amazing cover of "Running Up That Hill" is fucking PERFECT for the events of "In My Time of Dying." So much angsty!hurty!Dean and John love in this. Literally gave me chills. And it makes me want to go rewatch every single episode.
Renegade (Styx) by staceey. Sam & Dean's greatest hits in police custody
Dream On (Aerosmith) by LadyGhostWhisperer. Some wee!Dean and Sammy and some Psychic!Sammy tie into the "Dream On" theme.
This Dream On vid, which is John-centric, while not having much to do with actual dreams, matches the intensity of the song better. And the lines, "Every time I look in the mirror/all these lines in my face getting clearer." Interestingly, both vids use John's book for the lyrics "all my life in books and in pages."
Numb (Linkin Park) Maybe an obvious song choice, but it fits Dean perfectly, especially the footage from early Season 2, like "Bloodlust." Good, solid vid.
Okay, one more. Metallica's I Disappear is the perfect theme song for Badass Daddy Winchester.
ETA: Bad Company vid. Wow. This is SUCH a Winchester song. And the vid is edited so professionally and the action is synched up perfectly with the song, which I'm usually not a stickler for since it never happens. Here it does. And it's GUN PORN. Dean + Sam + Colt and every other kind of gun. *needs to be alone with vid*