These are my rankings based on the reviews. They are separated only by category. Within each category they are listed chronologically. In other words, the last one on the list is not necessarily the worst episode. (It could be any of the ones within the bottom group.)
1 - Very Top
0-P01 The Cage
1-P05 The Enemy Within
1-P08 Charlie X
1-P09 Balance of Terror
1-P13 The Conscience of the King
1-P16 The Menagerie (Parts 1 and 2)
1-P28 The City on the Edge of Forever
2-P42 The Trouble With Tribbles
2-P44 Journey to Babel
3-P56 Spectre of the Gun
3-P59 The Enterprise Incident
2 - Top
1-P02 Where No Man Has Gone Before
1-P03 The Corbomite Maneuver
1-P04 Mudd's Women
1-P18 The Squire of Gothos
1-P24 Space Seed
1-P23 A Taste of Armageddon
2-P34 Amok Time
2-P39 Mirror, Mirror
2-P40 The Deadly Years
2-P47 Obsession
2-P53 The Ultimate Computer
3-P66 Day of the Dove
3-P78 All Our Yesterdays
3 - Middle-Upper
1-P11 Dagger of the Mind
1-P15 Court Martial
1-P17 Shore Leave
1-P19 Arena
1-P26 Devil in the Dark
1-P27 Errand of Mercy
2-P31 Metamorphosis
2-P41 I, Mudd
2-P54 The Omega Glory
3-P58 The Paradise Syndrome
3-P63 The Empath
3-P71 Whom Gods Destroy
4 - Middle
1-P06 The Man Trap
1-P07 The Naked Time
1-P12 Miri
2-P38 The Apple
2-P45 A Private Little War
2-P48 The Immunity Syndrome
2-P49 A Piece of the Action
2-P51 Return to Tomorrow
2-P55 Assignment: Earth
3-P62 Is There In Truth No Beauty?
3-P72 The Mark of Gideon
3-P77 The Savage Curtain
3-P79 Turnabout Intruder
5 - Middle-Lower
1-P14 The Galileo Seven
1-P21 Tomorrow Is Yesterday
2-P33 Who Mourns for Adonais?
2-P35 The Doomsday Machine
2-P36 Wolf in the Fold
2-P43 Bread and Circuses
2-P52 Patterns of Force
3-P57 Elaan of Troyius
3-P64 The Tholian Web
3-P73 The Lights of Zetar
3-P74 The Cloudminders
6 - Bottom
1-P10 What Are Little Girls Made Of?
1-P22 Return of the Archons
1-P25 This Side of Paradise
1-P29 Operation: Annihilate
2-P30 Catspaw
2-P37 The Changeling
2-P46 The Gamesters of Triskelion
2-P50 By Any Other Name
3-P60 And the Children Shall Lead
3-P65 For the World is Hollow...
3-P68 Wink of an Eye
7 - Very Bottom
1-P20 The Alternative Factor
2-P32 Friday's Child
3-P61 Spock's Brain
3-P67 Plato's Stepchildren
3-P69 That Which Survives
3-P70 Let That Be Your Last Battlefield
3-P75 The Way to Eden
3-P76 Requiem for Methuselah