"Take a Dare"/Gilligan says "Sorry about that, Chief" to the Skipper.
"The Invasion"/ Ginger says "Sorry about that, Chief" in the dream sequence. That line came from Get Smart.

"Ring Around Gilligan"/ Dr. Balinkoff says "Be neat, sweet, petite" at the lagoon.
That came from the theme song for The Addams Family.

Not quotes from the show but a quote about the show.

FRASIER: Now, why is Gilligan magnetised?

LILITH: Because he was struck by lightning. Every time this episode airs you ask that question.

Nice to know a well respected psychiatrist like Frasier Crane watches the show.

This one isn't from the 1960's but I thought it was funny...
(From That '70s Show Red Forman watching "Gilligan's Island", as Kitty looks on)

Red: "Awwww... Gilligan screwed it up. Why don't they just kill him?"

Ohio8, I do recall that also. Funny that it was written into the script.
If Don Adams were not doing Get Smart, he would have fit right in as
one of the guest visitors to Gilligan's Island.

This one isn’t from the 60s either, but it’s from Newhart:

Susan Polger: Who do you think the Professor liked best? Mary Ann or Ginger?
Michael Harris: Well, Ginger had all those great gowns. But I used to love when Mary Ann would get on that bike and make electricity.

One I caught recently from the "Perfect Strangers" episode "Babes in Babylon" (1986).

Balki's sitting on the couch watching TV.

Balki: Watch out, Gilligan! Skipper's got a frying pan.

The Andy Griffith Show:

Barney Fife: If there's anything that upsets me, it's having people say I'm sensitive.

The Stand-up and Win skit on SNL with Seinfeld was a Jeopardy-like game with a Gilligan's Island category, which they use to do a good parody of the Gilligan's jokes stand-up comedians were doing back in the '80s.

https://www.youtube.com/watch?v=AsJYmf_G5d0

There was another '90s SNL skit, technically a commercial parody for an episode of "Gilligan's Bio-sphere." It seems to be the only Gilligan skit they've ever done. It's in this episode at 46:01:

https://archive.org/details/saturday-night-live-s-18-e-07-sinbad-sade