It's good to know what's bad : )
In Dungeon Keeper 2 there is a Moon level that appears on New Moon, and at the New Year, creatures dance and sing in the casino. Plus if you play from midnight till one, the game lector says "It is the witching hour. All curses are half price."

I'm bringing the thread up again since Halloween is approaching and thanks to the help of the community we know that there are about twenty games on GOG that have special events for Halloween.

If you know of any others or the dates have errors let me know!

Arma Cold War Assault (ex-Operation Flashpoint : Cold War Crisis) : If the system clock reports a date of December 25, some trees in the game world are replaced by decorated Christmas trees with presents.

Very interesting, just the kind of things I'm looking for, thank you!

Rise of the Triad has hats for each of the five characters on different holidays, including Halloween:
Easter <varies> Lorelei Ni wears Easter Bunny ears.
Cinco de Mayo 05/05 Ian wears a sombrero.
Independence Day 07/04 Doug holds an American flag.
Halloween 10/31 Thi wears a witch's hat.
Christmas 12/24-25 Taradino wears a Santa Claus hat; new music for the first level.

Raptor: Call of the Shadows has changes to the game on certain developers' birthdays, I don't know if it still worked on the version that was available on GOG:
http://www.rinkworks.com/apogee/s/6.3.2.shtml

Cave Story has a holiday mode, but you should not engage with the Nicalis version. They are thieves who paid Pixel none.