Well the ones I have been watching recently (or stopped so that I won't get sick of them) are:
"Got Melee?" which is Super Smash Bros : Melee done to "Basketcase" by Green Day, made by Six Sided Video at
http://www.geocities.com/professional666/index.html
"Sakura no Yume" which is Cardcaptor Sakura, made by Jeff Lawson at
http://www.jefflawson.net/nowhere
The above to is mainly for my almost 2 year old nephew, espeacially "Sakura no Yume" as it helps get him to sleep when he is in a terrible mood at night
I think someones already mentioned Speed King, Failed Experiments In Video Editing and Session 02 vid by SpPanda
Aluminum-"Try"
"Deluxe" which is Trigun done to "The deluxe war baby" by Burning Airlines, edited by Kwasek at
http://morethantoast.com
"Nightwish" which is Mobile Suit Gundam: The 08th MS Team edited by Danniel Cecava at
http://rubyeye.laughingsquid.org/
Studio Hybrid - Jinnai and the Bugrom Live
Lostboy-Rhythm Animation-Two Mix-Various, as it gives my older brother a head ache.
Ikasu Smoothe Studios - Enigma