One of my favorite games, and one of my... well, he's not one of my absolute favorite writers, but as an old-school New Englander he's my boy: H. P. Lovecraft. In Oblivion, there is a questline called "A Shadow Over Hackdirt" which, as pointed out in various wiki entries, is an homage to Lovecraft's "The Shadow Over Innsmouth." A town! A dark secret! Mystery! Note that, according to the Wikipedia page, "The Shadow Over Innsmouth" is based on other stories. Culture begets culture.
One of the Oblivion wikis also has a list of easter eggs, many of which are homage.
I mostly focus on homage in EverQuest 2, since there is so much of it, but people like to play with the things they like, so homage shows up in a lot of game spaces.