One of the better examples is the wedding of Mary Jane and Peter Parker, done because Stan Lee wanted to marry them in the daily newspaper comic strip. Of course, that didn't stop Tom Brevoort from claiming that One More Day was actually a "fix" to this form of "meddling".
What Could Have Been: Stan Lee has gone on record as saying if Gwen Stacy hadn't been killed off, most like she would've ended up married to Peter. Some stories, like House Of M, have toyed with this idea.
Joe Quesada wanted to bring Gwen back from the dead in Brand New Day but it was decided against.
Young Allies offered Anya Corazon a potential chance to shine. It had a cast with the potential to create a very interesting character dynamics, and which Anya shone through as the most down to Earth, and easiest to relate to character. But it was killed by poorly written out enemies, an uninteresting and almost generic story arc, and a refusal by Sean McKeever to give the team any sort of cohesion in spite of their common purpose and motivations.
It really seemed the team was finally coming together by the 5th issue or so, but by then the series was canceled. The Young Allies have been popping up here and there however, most recently in Spider-Island.
Serendipity Writes The Plot: Technical difficulties meant that they had to render the city in as less a difficult a way as possible. So they explained in-story that New York got covered in fog by a machine made by Doctor Octopus.