Ugh, I spent way too much time today thinking about this. My criteria was: like the Baseball HOF, you can only get in under one team (like why Randy Johnson is going into the HOF as a Diamondback, not a Diamondback and a Mariner), so each song only gets in once with one definitive (to me) version. (None of this 2 Tweezers, etc.). Nothing within the last 5 years makes the list or is even considered, the way a baseball player needs to be retired for 5 years before being voted on for the HOF. And tunes can have a -> (they don't need to be a standalone). So, my list is:

11/2/94 Tweezer
12/29/94 David Bowie
6/26/95 Down With Disease
12/9/95 You Enjoy Myself
7/23/97 Ghost
4/3/98 Roses Are Free
7/29/98 Bathtub Gin
11/2/98 Tube
12/31/99 Crosseyed & Painless
8/3/03 Chalkdust Torture

Honorable Mentions (which could have included another 50 tunes): 11/22/97 Halley's, 11/29/97 Runaway Jim, 12/13/97 Ya Mar, Hood, 12/30/97 AC/DC Bag, 12/31/97 Emotional Rescue, 4/2/98 Twist, 4/3/98 Mike's, Piper, Antelope, 10/30/98 Antelope, 12/29/98 2001, 12/4/99 Melt, 12/31/99 Sand, Reba, David Bowie, Drowned, Roses Are Free, 7/15/00 Down With Disease, 6/24/04 Tube