Edge of Tomorrow, the movie where tom cruise is put in a weaponized time loop to stop an alien invasion, stars a female lead named Rita that the male lead pines and tries to earn the love of. This is a reference to Groundhog Day's female lead named Rita.
I kinda wished that they had named the male and female leads named Phil Connors and Rita Hanson, so that it could be interpreted as the weirdest AU fan-work of Groundhog Day ever.
Marvel's Deadpool (Wade Wilson) was initially a parody of DC's Deathstroke (Slade Wilson).
JoJos Bizarre Adventure has a sizable chunk of characters whose names are 80s bands or musicians.
Quite a few stories have biblical names or classical god names for their characters when not depicting the original, but that's even more of a stretch than my other examples.
They let Larry Niven write some episodes of Star Trek: The Animated Series, so now the K'zinti (cat people Niven originally introduced in his Ringworld stories) are canon in the Star Trek Universe. The producer (or maybe director, I don't really remember) of those cartoons was color blind and as a result, those cat like aliens became cannonicaly purple.
Aww jeez, that's got to suck. Not the crossover part, that's awesome, but the fact someone who is colorblind and might not know it would be put on the spot like that. As an artist, I notice a lot of people from the colorblind community pop up and need help with creative feats that come normally to other people, and I don't have the heart to expect anything in response.
Bastard. Lots of heavy metal references. Bon Jovina is the head knight of Meta-llicana. There is a Megadeath spell. Osbourne attacks the kingdom. Lots of others I don't remember.
Not quite what you're asking for but in Douglas Addams' Restaurant at the End of the Universe, there's a side character called Hotblack Desiato which is the name of the estate agent in Islington that Addams walked past to get to his office each day and he liked the name so much he created the character around it.
A very different example would be the character Alfred Bester from Babylon 5. B5's Bester is the main "Psi Cop" in the show — a strong telepath who enforces the strict laws on other telepaths. He is named for the science-fiction author Alfred Bester, whose novel The Demolished Man established several of the telepathy tropes that are used in B5, including the existence of a formal organization that manages telepaths and telepath/mundane relations: in the novel it's called the Esper Guild, in B5, it's the Psi Corps.