Since you're covering the whole series, here's my best and worst list, minus Enterprise, which I have not overviewed thoroughly enough to make a list yet.
Best of Star Trek series:
TOS:
1. Balance of Terror
2. The Doomsday Machine
3. Conscience of the King
4. City on the Edge of Forever
5. A Taste of Armageddon
6. Devil in the Dark
7. The Naked Time
8. Mirror, Mirror
9. Journey to Babel
10. Arena
STNG:
1. Best of Both Worlds I and II
2. Yesterday's Enterprise
3. Darmok
4. The Inner Light
5. The Chase
6. The Measure of a Man (Extended)
7. The Survivors
8. The Wounded
9. Q Who
10. Where No One Has Gone Before
DS9:
1. Duet
2. Emissary
3. Captive Pursuit
4. In the Hands of the Prophets
5. The Visitor
6. The Abandoned
7. Rocks and Shoals
8. A Call to Arms
9. The Quickening
10. In the Pale Moonlight
VOYAGER:
1. Distant Origins
2. Blink of an Eye
3. Critical Care
4. Caretaker
5. Scorpion I and II
6. Deathwish
7. Living Witness
8. Child's Play
9. Deadlock
10. Prototype
11. Think Tank
12. Remember
13. Relativity
14. Pathfinder
15. Timeless
16. Equinox I and II
17. Dark Frontier I and II
18. Drone
19. Prey
20. Memorial
ENTERPRISE:
THE WORST:
TOS:
1. Plato's Stepchildren
2. Turnabout Intruder
3. The Mark of Gideon
4. And the Children Shall Lead
5. The Way to Eden
6. Whom Gods Destroy
7. Spectre of the Gun
8. The Lights of Zetar
9. Spock's Brain
10. The Apple
STNG:
1. Shades of Gray-Kind of useless except for budgetary reasons.
2. Emergence-Single most pointless episode of STNG. Nothing redeems it.
3. Man of the People-Almost unwatchable.
4. Manhunt-Needless, less charming retread of Haven.
5. The Loss-The Betazoid pms episode...this was not ST. Even a fairly cool 2D alien couldn't save this episode.
6. The Royale-Had about 15 good minutes in it about Colonel Richie, but ultimately not very good.
7. Samaritan Snare-It wasn't only the Pakleds who were dumb in this episode. Nominated for worst aliens ever in a Trek series.
8. Haven-A few good character moments, not much else.
9. Rascals-Silly
10. Laisons-Non-sensical
Honorable mention: Realm of fear. Horrible ending and technobabble.
DS9:
1. Fascination
2. Profit and Lace
3. Dax
4. If Wishes Were Horses
5. Looking for Parmach..
6. The House of Quark
7. Ferengi Love SOngs
8. Meridian
9. Family Business
10. Our Man Bashir
11. Let He Who is Without Sin
VOYAGER:
1. Threshold
2. Twisted
3. Sacred Ground
4. Favorite Son
5. Coda
6. The Thaw
7. Persistence of Vision
8. Elogium
9. Darkling
10. Scientific Method
ENTERPRISE:
Worst overall: Threshold
RAMA
Best of Star Trek series:
TOS:
1. Balance of Terror
2. The Doomsday Machine
3. Conscience of the King
4. City on the Edge of Forever
5. A Taste of Armageddon
6. Devil in the Dark
7. The Naked Time
8. Mirror, Mirror
9. Journey to Babel
10. Arena
STNG:
1. Best of Both Worlds I and II
2. Yesterday's Enterprise
3. Darmok
4. The Inner Light
5. The Chase
6. The Measure of a Man (Extended)
7. The Survivors
8. The Wounded
9. Q Who
10. Where No One Has Gone Before
DS9:
1. Duet
2. Emissary
3. Captive Pursuit
4. In the Hands of the Prophets
5. The Visitor
6. The Abandoned
7. Rocks and Shoals
8. A Call to Arms
9. The Quickening
10. In the Pale Moonlight
VOYAGER:
1. Distant Origins
2. Blink of an Eye
3. Critical Care
4. Caretaker
5. Scorpion I and II
6. Deathwish
7. Living Witness
8. Child's Play
9. Deadlock
10. Prototype
11. Think Tank
12. Remember
13. Relativity
14. Pathfinder
15. Timeless
16. Equinox I and II
17. Dark Frontier I and II
18. Drone
19. Prey
20. Memorial
ENTERPRISE:
THE WORST:
TOS:
1. Plato's Stepchildren
2. Turnabout Intruder
3. The Mark of Gideon
4. And the Children Shall Lead
5. The Way to Eden
6. Whom Gods Destroy
7. Spectre of the Gun
8. The Lights of Zetar
9. Spock's Brain
10. The Apple
STNG:
1. Shades of Gray-Kind of useless except for budgetary reasons.
2. Emergence-Single most pointless episode of STNG. Nothing redeems it.
3. Man of the People-Almost unwatchable.
4. Manhunt-Needless, less charming retread of Haven.
5. The Loss-The Betazoid pms episode...this was not ST. Even a fairly cool 2D alien couldn't save this episode.
6. The Royale-Had about 15 good minutes in it about Colonel Richie, but ultimately not very good.
7. Samaritan Snare-It wasn't only the Pakleds who were dumb in this episode. Nominated for worst aliens ever in a Trek series.
8. Haven-A few good character moments, not much else.
9. Rascals-Silly
10. Laisons-Non-sensical
Honorable mention: Realm of fear. Horrible ending and technobabble.
DS9:
1. Fascination
2. Profit and Lace
3. Dax
4. If Wishes Were Horses
5. Looking for Parmach..
6. The House of Quark
7. Ferengi Love SOngs
8. Meridian
9. Family Business
10. Our Man Bashir
11. Let He Who is Without Sin
VOYAGER:
1. Threshold
2. Twisted
3. Sacred Ground
4. Favorite Son
5. Coda
6. The Thaw
7. Persistence of Vision
8. Elogium
9. Darkling
10. Scientific Method
ENTERPRISE:
Worst overall: Threshold
RAMA