Gilligan vs. the ghost (when someone was trying to scare the castaways off the island)
Gilligan vs. the Dragon (when he thought the weather balloon was a monster)
Gilligan vs. Vampirism (when Gilligan got bit by a bat, he thought he would change into a vampire)
Dr. Gilligan vs. Mr. Hyde (Gilligan dreams that he is a Dr. Jeckyll and Mr. Hyde when the castaways disappear one by one)
Gilligan vs. the giant spider
Gilligan vs. the invisible man (when Gilligan gets struck by lightening, he became invisible)

Near the end of one episode, doesn't Gilligan bump into Skipper and calls to the Skipper "is that you?" and the Skipper stretches out his arms and says "No, it's Frankenstein's monster" and chases Gilligan off?

Does anyone recall this? Perhaps which episode it was?

Just found the transcripts on the Gilligan Island Fan Club site. It was "Up at Bat" episode.

Gilligan vs the Mummy if you count the episode where the Professor wraps Gilligan in medicated bandages to make him visible again.

WOW!