I'm digging deep into my memories to sort this out.
My earliest brickfilm memories all include the following films, which I saw either right before or just after I discovered Brickfilms.com in 2001 or 2002. All of these films have pages on the Brickfilms Wiki.
The Rescue by Jason Allemann
Haunted by David Pagano
The LEGO-produced brickfilms for LEGO Studios, like Dino Cop.
After discovering Brickfilms.com, I strongly remember:
ONE: A Space Odyssey by Spite Your Face
Also Thwacked Zarathustra and The Big Match by Thomas Foote
Sector 7 by Robert Taylor
Great Inventors Part 1: The Wheel by Stefan van Zwam
Zero Gravity Rebellion and The Letter by James Maduzia
Of these, Sector 7 is unique. I don't think I'm exaggerating in stating that I might be the only person who remembers Sector 7. For some reason, it left an impact on me as a kid, and I distinctly remembered it for many years. In fact, it was the film that inspired me to start the Brickfilms Archival Project, because I thought Sector 7 was lost to the abyss. Amazingly, Penta was able to help me track it down.