>>6"From Yesterday" - 30 Seconds To Mars (but pretty much all of 30STM's vids are fantastic)
"Vicarious" - Tool (but all of Tool's vids are badass too)
"Human Gift" - LITE (and all of LITE's vids are pretty awesome too...I'm noticing a pattern here)
"Krwlng" (Crawling Reanimation Remix) - Linkin Park (stunning visuals, perfect music, shame there isn't a better quality version on the Youtubes)
"Warning" - Green Day (lolsy premise is lolsy)
"This Too Shall Pass" - OK GO (a music video list isn't complete without these guys)
"Hope" - Cyclamen (consists of video of the aftermath of the Japanese earthquake in 2011- Hayato's uplifting falsetto matches the visuals perfectly)
"Make Total Destroy" - Periphery (we're talking about my taste here, I mean, come on)
"Finale" - Anoice (chilling vid/song combo)
Fear Of A Blank Planet - Porcupine Tree (The 40-year olds hit the nail on the head for the troubled adolescents of the present: a.k.a. why we can't have nice things. Brilliant cinematography)
"Roadie" - Tenacious D (we're talking Jack Black here, can it ever actually go wrong?)
and for fan-made music vids:
"Same Ol' Road - Dredg (as a commenter says, looks like a pro clip)
"Circles - Thrice (It's got Charlie Chaplin's Great Dictator speech over the music: amazing)
That's all I can think of right now, might post some more later if they come to mind.