Well, I can try another. For most of 3.0 and 4.0, I don't know enough to come up with a decent list! But here's one for '03:

Song: 12/31/02 Piper
Why: Return from the hiatus; excellent, fiery jam with some elements that are typical of this era; it very obviously marks a new beginning for the band
Length: 15 minutes

Song: 1/2/03 46 Days
Why: The up tempo, rollicking funk jam is common in several other 2.0 improvisations--see 6/20/04 Drowned is the only one that springs to mind--with a strong acceleration jam
Time: 5 minutes

Song: 2/14/03 Bathtub Gin, blissy jam
Why: The first really magnificent improvisation post-hiatus, at least to my ears (though I am sort of a defender of the MSG / Hampton run); the climatic bliss jam is both wonderful in itself and anticipates a lot of the jamming of this year
Length: Let's say 8 minutes

Song: 2/16/03 Viper, jam near the end
Why: The calypso-style funk jamming is a fine representation of a style--Trey playing chords, funky rhythm behind him--that the band would revisit several times in the next couple of years; the 2.0 permutation of the funk, if you like; see 2/22/03 Tube, several YEMs, 2/26 Stash in part, several Pipers from the summer, the 7/18 DWD, and many other jams I'm sure; sort of similar in feel to the 1/2 46 Days but funkier and without as much of an acceleration jam
Length: 8 minutes

Song: 2/22/03 WOTC
Why: There are a lot of very fiery jams from this eras that are not very melodic but just rip into this hazy, wild space, especially coming from some of the Round Room songs; see, e.g., other versions of WotC, 2/20 Pebbles, and others I think; maybe even the 7/29/03 C&P has this feel?
Length: 8 minutes

Song: 2/28/03 Tweezer, bliss jam starting aroudn 14
Why: Similar in kind to the 2/14 Gin but probably better; one of the legendary jams in Phishtory, and the definitive 2.0 Tweezer
Length: 8 minutes

Song: 7/15/03 Mr Completely
Why: Idunno, it's really good, people really like it, I really like it, it's HOSE, it's the first time Phish played Mr C, but I don't really know
Length: 10 minutes maybe? I don't really know.

Song: 7/22/03 Gumbo
Why: The somewhat down-tempo bliss jam--I think people call it an "Oxy" jam--has something in common with the 2/14 Gin but opens up some new space; the 8/10/04 Birds will sound a lot like this in a more up-tempo way; definitely representative of a certain style
Length: Say 7 minutes around the end

Song: 7/25/03 Hood
Why: It's helpful to hear how they wove in an out of a melodic song like Hood in an era when they were playing a lot of shreddy hazy stuff; this is a VERY diverse jam, and i guess I mostly recommend the end for that reason. But the whole thing should be heard.
Length: 10 minutes

Song: 8/2/03 Waves, jam at the end
Why: That terrifying jam at the end captures something unique that you'd see here and there in jams, when they really went all-in for something SCARY; also good to have something representing IT. There was some other scary stuff that weekend too (DWD, 46 Days, e.g.; this is typical)
Length: 8 minutes

Song: 12/28/03 Suzy
Why: Shreddy heavy metal jam is another place the band would go sometimes those days
Length: 10 minutes

There's plenty more to include, but there's another stab at a year in 100 minutes. Not a list of the best jams, nor even something that represents the best tours, but I've tried to pick stuff that shows where the band was going that year.