Pitchfork's 100 Awesome Music Videos, complete with - you guessed it - videos. Some of the video files aren't there anymore, but most are.
Stylus magazine has their top 100 music videos of all time, too. This one is more mainstream than Pitchfork's, but there is just enough overlap on these two lists to be interesting.
Some of my favorite videos, from those lists or not, are:
The Child - Alex Gopher
Font as a character.
Frontier Psychiatrist - The Avalanches
Where's Your Head At? - Basement Jaxx
Monkeys with instruments.
Float On - Modest Mouse
Cool moustache, and even cooler Loretta Lynn look-alike.
Closet Freak - Cee-Lo
Before there was Gnarles, there was Soul Train.
Burnin' - Deft Punk
Is that a groove, or a fire alarm?
Danger! High Voltage! - Electric Six
Remember the Tra-la-la guy? I think that's him. Actually, it's rumored to be Jack White, which is just as cool. This is the best train-wreck of a video ever.
First Day of My Life - Bright Eyes
Lovers in love.
Hurt - Johnny Cash cover of Nine Inch Nails
Fitting tribute and autobiographical account of the Man in Black.
It's Oh So Quiet - Bjork
All musical theatre-y.
Can't Get You Out of My Head - Kylie Minogue
That white dress/pantsuit/curtain is mesmerizing.
Imitation of Life - R.E.M.
Kind of like a Where's Waldo, only with weird people.
Wild Wild Life - Talking Heads
John Goodman in a leisure suit. And David Byrne.
Weapon of Choice - Fatboy Slim
Walken channels his inner Gene Kelly.
Love is a Battlefield - Pat Benatar
Thriller, but with 80s punk bitches instead of zombies.
Vidrar Vel Til Loftarasa - Sigur Ros
Beautiful and devistating.
Drop - The Pharcyde
Spike Jonze does it backwards.
Once in a Lifetime - Talking Heads
A seriously stressed out David Byrne.
Star Guitar - The Chemical Brothers
Landscape was percussion.
Sledgehammer - Peter Gabriel
Sure you've seen it. Watch it again now that you are older and enjoy it even more. While your'e at it, see Death Cab for Cutie's homage to this video with their Crooked Teeth.
Bad Cover Version - Pulp
Like Band Aid on a budget.
Rabbit in Your Headlights - U.N.K.L.E. featuring Thom Yorke
Sad, powerful, and ultimately very moving.
We Will Become Silhouettes - The Postal Service
An early 80s childhood brought to life, except for the gravy drinking.
Such Great Heights - Ben Folds cover of Postal Service
If there is a musical equivalent of Hollywood, Ben Folds should be the fucking emperor.
For more excellent music videos, check out David LaChapelle's video page, which contains the excellent "This Train Don't Stop There Anymore" vid, which is linked to but missing from Pitchfork's list.
Also, see this excellent rendition of Radiohead's ode to moroseness, Creep.
Finally, Kenna's Hell Bent video is one of my all-time favorites.