I've provided a link to those that are on the .org, but not available for download. I'm not 100% sure on all of the links, but I've put down the most likely candidate for the video I'm looking for in those cases.
Ah! My Goddess OAV - Tal Bachman - She's So High
Chobits - Linkin Park - Frgt10
Chrono Cross - Nine Inch Nails - Even Deeper
Chrono Cross - Staind - Outside
Elfen Lied - dirtymopwater - Mindless Self Indulgence - Shut Me Up
Fatal Frame - Sentai Otter - King of Fighters Best Arrangement - Rhythmic Hallucination
Fruits Basket - Amanda Marshall - Sunday Morning After
Gravitation - Hamptom the Hamster - The Hamster Dance (techno remix)
Kare Kano - Dave Matthews Band - Crash
Love Hina - Senta Miller - Offspring - Come Out and Play
Parasite Eve - Fear Factory - Shock
Parasite Eve - Lunatic Calm - Leave You Far Behind
Parasite Eve 2 - Alice Cooper - Poison
Parasite Eve 2 - Linkin Park - Crawling
Pokemon - Aluminum Studios - New Order - True Faith
Resident Evil and Silent Hill - Marilyn Manson - Sweet Dreams
Resident Evil - android18 - Garbage - As Heaven is Wide
Resident Evil - The Offspring - The Kids Aren't Alright
Resident Evil 3 - The Offspring - Come Out Swinging
Sailor Moon - Fuel - Innocent
Silent Hill 2 - Staind - It's Been Awhile
Silent Hill 2 and 3 - Disturbed - Remember
Tokyo Babylon - Vast - Pretty When You Cry
Trigun - Bon Jovi - Wanted, Dead or Alive
Trigun - Kid Rock - Cowboy
Trigun - Pearl Jam - Jeremy
Various Anime - Blackmore's Night - Wish You Were Here
Various Anime - Gabrielle - Dreams
Various Anime - Mary J. Blige - No More Drama
X 1999 - Marilyn Manson - Cryptorchid
Yami no Matsuei - Dido - Hunter
Yu-Gi-Oh! - The Mad Psyentist - Luna Sea - Claustrophobia
Yu-Gi-Oh! - Yoo Seung Jun - Korean Rap
A few of these might still be floating in The Vault and I missed it, but since I don't know videos by editor, it's tough to track 'em down.
Thanks for any help you can offer.

- Jen