These are things that I can't devote a whole post to, but are worth mentioning anyway:
1. Lois Lane was first depicted as naming Superman in Superman: The Movie (1978), which has since gone on to appear in various depictions of Superman's origins in the comics.
2. Spider-Man's upcoming sidekick, Alpha (who makes his first appearance in Amazing Spider-Man #692), has the real name "Andrew Maguire", which is a reference to Spider-Man actors Andrew Garfield and Tobey Maguire.
3. Alfred was first depicted as raising Bruce Wayne in the Super Powers episode, "The Fear" (1984), and that part of the origin would make it to comics - perhaps coincidentally, mind you, but still later - in The Dark Knight Returns and Batman: Year One.
4. "The Narrows", the poor part of Gotham as depicted in Batman Begins has since appeared in the New 52 Batman comics. It was first mentioned in Batman: Dark Knight #2 (October 2011).