This is a tough question because there's so many great ones to pick from, but I'll base my selections on how much I like the song AND the video. There's a lot of amazing videos to songs I hate, so I don't include those. Here's a short list...
The Mighty Mighty BossToneS - "Kinder Words"
- Video was based on the movie Cool Hand Luke, and happens to be one of my favorite songs by my favorite band
Naive New Beaters - "Live Good"
- Amazing video with amazing use of green screen
Protest The Hero - "Heretics and Killers"
- Awesome song, even more awesome video
Bush - "Greedy Fly"
- Good song, EPIC video
Meat Loaf - "Object In The Rearview Mirror May Appear Closer Than They Are"
- I'm a big fan of Meat Loaf's Bat Out Of Hell II album, and this was my favorite song, and also the most epic. The video was also directed by Michael Bay and featured Robert Patrick