The greatest funk track of all time is Funkadelic's "(Not Just) Knee Deep", by far, but here are some of my favorites (all on my iPod right now), some of them are not necessarily well-known tracks, but check them out:
Bootsy Collins-The Pinocchio Theory
-Can't Stay Away
Gap Band-Burn Rubber (Why U Wanna Hurt Me)
-Humpin'
Parliament-Agony of Defeet
-Dr. Funkenstein
Prince-I Feel 4 U
-Musicology
Rick James-Below the Funk (Pass the J)
-Ghetto Life
Roger-A Chunk of Sugar
By the way, I was always a fan of Quik's instrumental tracks (Grooves & Reprises), funk fans should check out Quik's "Hoorah for the Funk (Reprise)", straight funk, I just wish it was longer than 2:00.