First, thanks to @TheRealBurnham for making this happen, I'm surprised it hasn't been done before, and I'm a little bummed that I missed the boat on the voting and am late to the show with comment. That said, a few things:

1.) Tahoe Tweezer: I'm with most in agreeing that there's this doesn't belong at the #1 slot (it wouldn't make my top 30, or even my top 3 of 3.0 for that matter), but I agree with @squail that it is likely due to the relatively narrow selection pool for 3.0 "all-time jams" vs. the vast selection pool for 1.0, and most people not wanting to exclude 3.0 completely thus the token single vote for Tahoe. It's the only way this makes sense. It's still a great, great jam though.

2.) Notable omissions (off the top of my head):

Reba!!! Not one version?!? 8/16/93, 7/6/94, 10/31/94, or 5/16/95 all are worthy candidates
Divided!!! Several versions from 93-95 are worthy (6/18/94, 10/31/94 and 10/31/95 are my Top 3)
2001!!! One of these should probably be noted: I'd go with Gorge 98, MSG 98, or Memphis 99
12/30/93 Mike's - thematic, melodic, concise, dark, intense, with a perfect, dream-like segue into Horse. So much goodness in this one
11/12/94 Hood - to me, head and shoulders above 12/31/93 (which I think is similarly great but slightly overrated). Jam starts off with a couple quiet moments, then builds slowly into a rumbling out of control freight train (Fish just goes off on this one), then virtuostic Trey followed by a glorious double peak. Unparalleled version (although A Live One version comes close, as does 7/1/95).
11/26/94 Bowie - as good or better than Providence, IMO
11/28/94 Tweezer - to me, the pinnacle of their early "Type II" jamming
6/16 or 6/26/95 Jim
12/1 or 12/7/95 Mike's Groove
12/14/95 Tweezer> Timber> Tweezer or Halley's> NICU - this is one where the entire set should just count as one entry. Hot, hot stuff.
12/31/95 Drowned or Jim
10/26/96 Simple (I'm with @frankstallone on this)
11/27/96 Diseazer
2/17/97 Carini - this is Tier 1 material IMO. Dark, frightening, and downright psychedelic in parts, then releases into a refreshingly gorgeous cooldown hosing at the end.
7/2/97 Stash - another Tier 1 contender. (Off topic: so stoked this is getting a official release!)
7/23/97 Ghost
7/30/97 Bowie> Cities> Bowie, as others have mentioned
8/13/97 Gumbo - shining example of 97-style cow-funk jamming
12/29/97 Theme - I'm with @VanillaTheHun on this. This hardly gets any mention, and sure it's squarely in the Type I mold, but the way Trey just wills this solo on, hitting several cool licks and mini-themes (we're talking, a couple measures then we're moving along here), then out of nowhere builds into one the most orgasmic, 30-second long guitar peaks ever caught on tape. There really isn't another version that compares with this one. If there was a Type I HoF this would be Tier 1 w/o a doubt!
4/2/98 Twist - for me, THIS was The Jam of the Island Tour
7/2/98 Ghost - depending on which day of the week it is, I like this better than the Prague ghost
7/24/98 Wolfman's - underrated and possibly my all-time favorite version
8/1/98 Tweezer - so much gorgeous jamming in this one
11/6/98 Split - one of the most locked-in, funkiest grooves they've ever played (and that's saying a LOT!). Maybe not "out there" enough for inclusion w/ some of the others on this list, but a definite shoe-in for the Type I HoF.
12/28/98 Carini> Wolfman's - funky & dark, with lots of the signature 98 ambient jamming thrown in.
12/7/99 Halley's - possibly Tier 1 material IMO, especially in the last 10 minutes of the jam. The bliss section that winds its way into the beautiful ambient-style finish makes me see all that is beautiful and right in the world. Would take this over 11/22/97 any day of the week.
12/16/99 Tweezer - not sure if it belongs given all the amazing versions, but definitely better than 2/28/03 IMO.
12/30/99 Mike's - the most face-melting version of any song they've ever played merits a slot in the HoF. There are few things I can listen to that make me feel like I'm in a totally altered state like this one can.
12/31/99 Sand > Quadrophonic Toppling - I'll go with @n00b100 on this, there's too much good jamming from Cypress to mention, but if I were forced to pick just one...
6/9/00 Tweezer - soooo underrated this one. A half-hour head trip that covers so much ground.
6/29/00 Drowned > Rock & Roll as others have mentioned

I'm sure I missed a bunch of 1.0 nuggets (just thought of Chula Vista Boogie On, Van Andel Halley's, UIC '98 Gin & Bag...aagh!), but I'll stop there since I've gone on way too long, I'm more inclined towards 1.0 anyway. I do agree with most of the omissions others have mentioned for 2.0 and 3.0 though, particularly Gorge RnR, Dick's Light, MPP Light > Boogie On, Hampton Tweezer, Reading Disease, and Randall's CDT> Light.