This is a big list but here are my fave episodes. What are yours?

So Sorry, My Island Now
The Matchmaker
Forget Me Not
Music Hath Charm
Physical Fatness
My Fair Gilligan
Gilligan's Mother-in-law
A Nose By Any Other Name
Smile, You're On Mars Camera
Castaways Pictures Presents
Hi-Fi Gilligan
Gilligan Gets Bugged
Mine Hero
The Postman Cometh
Forward March
Ship Ahoax
Feed the Kitty
Will the Real Mr. Howell Please Stand Up?
Allergy Time
The Friendly Physician
"V" For Vitamins
The Invasion
Court-Martial
Gilligan's Personal Magnetism
The Second Ginger Grant
Slave Girl
Bang! Bang! Bang!

I really like them all, but these stand out for whatever reason.

Waiting for Watubi
New Neighbour Sam
Three to get Ready
Smile, You're on Mars Camera
Quick Before it Sinks
Castaway Pictures Presents
Hi-Fi Gilligan
Gilligan gets Bugged
Not Guilty
Seer Gilligan
Operation:Steam Heat
Up at Bat
Pass the Vegetables Please
The Producer
And then there were None
Court-Martial
The Hunter
Bang! Bang! Bang!

Waiting for Watubi has many great scenes. Including Maryann dressed as a native. As for New Neighbor Sam outstanding premise and the mystery is excellent.

Goodbye Island
Two in the Raft
Wating for the Watubi
So Sorry, my Island Now
X Marks the Spot
The Matchmaker
Physical Fatness
Beauty is and Beauty Does
Quick before it Sinks
Hi-Fi Gilligan
Don't Bug the Mosquitos
Mine Hero
You've Been Disconnected
The Postman Cometh
Feed the Kitty
The Friendly Physician
Up At Bat
Gilligan vs Gilligan
Pass the vegetables
And Then the were None
Gilligan's Personal Magnetism
Gilligan Goes Gung-Ho
The Producer
Bang Bang Bang
The Goddess