So according to the current Trek Mate Forum Community the best 20 episodes of Star Trek Are:

TOS

Galileo 7

Court Martial

TNG

Darmok

The Offspring

The measure of a Man

Yesterdays Enterprise

Chain of Command

All good things

DS9

Past tense p1 & 2

Its only a paper moon

Take me out to the Holodeck

Way of the warrior

Duet

VOY

Eye of the Needle

Distant Origin

Timeless

Equinox P1 & 2

ENT

Cese Fire

Twilight

Vox Sola

We will do this test again in a couple of months and probably get a completely different list