Official Sites:

Phish
Phish Dry Goods

Related Side Groups:
Trey Anastasio Band
Oysterhead
Vida Blue
Pork Tornado
Leo Kottke
Jazz Mandolin Project

Charity work:
Mockingbird Foundation
WaterWheel Foundation
Mimi Fishman Foundation

Archive Sites:
Phish.net
Phish Archive
The Runaway Golfcart Marathon
Phishpics.net

Poster Artists:
Jim Pollock
expressobeans

Fan Sites:
Phans.com
Andy Gadiel's Phish Page
Walfredo
Phantasy Phish
People for a Clearer Phish
ZZYZX
Phunky Bitches
Phellowship
Chris Kuroda

Trading/Forums:
news:rec.music.phish
Phishhook
Etree
DB.Etree
Also Vine Zarathustra
Furthernet