These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ensemble Dark Horse: Ginger was advertised as the celebrity sex symbol, and Mary Ann was the plain Kansas farm girl, yet the fans preferred her.
Everyone Is Jesus in Purgatory - The popular theory that the seven castaways represent the seven deadly sins, and that the island is a purgatory for them to work off their bad karma, or a hell constructed specifically to torture them.
Ear Worm - the theme song. As Achewood pointed out, Emily Dickinson's "Because I could not stop for Death" fits the theme song... as do "Amazing Grace", "Auld Lang Syne", and the first verse of the first English Pokémon theme.
The aforementioned works are all written in Ballad Meter if you're wondering.
Speaking of the show's music, the pilot's theme (and most of the series' early incidental music) was written by John Williams. Yes, the John Williams. That's also Sherwood Schwartz singing. Also counts as an Ear Worm.
Ho Yay - In one episode both Gilligan and the skipper both think the other has been turned into a monkey. It Makes Sense in Context. What is the first thing they do when they see the monkey dressed up in the other's clothes? Strip it naked, of course.
Apart from that, consider the Skipper's way of addressing Gilligan as "Little Buddy."
Hollywood Homely: Mary Ann. Even lampshaded on The Simpsons when the network executive wanted someone "ugly" like Mary Ann, not "ugly ugly" like Moe. (Even though none of the other Gilligan characters ever referred to Mary Ann as homely; more the shy, Girl Next Door type.)
Never Live It Down: Gilligan is so infamous for "always" accidentally ruining the Castaways' plans to get off the island that Just Eat Gilligan became a meme and then a trope. But a dedicated fan decided to watch every episode and make note of the number of episodes the castaways tried to get off the island and the number of those episodes where their plans were ruined by Gilligan. It turns out Gilligan bungles their plans in exactly 17 episodes. Which is still a lot, but it's less than half of the number of episodes the Castaways tried to escape, 37. More importantly, there were 98 episode total. So Gilligan botched the Castaways rescue/escape attempts less than half the time they tried and in only a little more than a sixth of all episodes.
Nightmare Fuel: More than one viewer felt that during the show's "Jack and the Beanstalk" dream-episode, Alan Hale was genuinely frightening as the giant.
"Ghost a Go-Go" uses the Bedsheet Ghost trope (albeit it's a man pretending to be a ghost) and while the episode mostly keeps it from being Nightmare Retardant, it doesn't quite reach this trope. There is, however, one scene in the episode where Gilligan is woken up by the "ghost", opens the blinds, and sees the guy standing right outside his window staring at him.
The Problem with Licensed Games: Why someone thought this would make a good video game is one of history's great unsolved mysteries, but a NES game was made. It's generally considered one of that console's worst titles.
Unfortunate Implications: Played with; while there is a spear-carrying bare-chested native with a bone in his nose holding a shrunken head, he's unambiguously pale with face paint that resembles Nerd Glasses.