New York City

Marvel Comics

Here are the major landmarks of NYC in the Marvel Universe:

• Daily Bugle Building - the major newspaper in which Peter Parker (Spiderman) works as a freelance photographer.

• Baxter Building - headquarters of the Fantastic Four.

• Avengers Mansion - destroyed, located 890 Fifth Avenue, home of the Avengers.
• Empire State University - Superheroes Peter Parker, Emma Frost, Johnny Storm ( Human Torch), Gwen Stacy and Reed Richards ( Mr. Fantastic) attended this university.

• Midtown High - High School of Mary Jane, Peter Parker, Harry Osborn, Liz Allen, and Flash Thompson.

• Stark Tower / Avengers Tower - owned by Tony Stark, but the Avengers use the top floor as their new headquarters, capped by the Sentry's watchtower
• Four Freedoms Plaza - Fantastic Four's headquarters between old and new Baxter Building, has been destroyed
• Hell's Kitchen - Crime fighting territory of Daredevil
• Morlock Tunnels - Located under NYC it was the home to the Morlocks, a group of mutant outcasts
• Ryker's Island - A real prison used in comics to hold super villains
• Sanctum Sanctorum - Mystical home of Doctor Strange
• Triskelion -  SHIELD headquarters located off coast of NYC

 
Coincidentally, Marvel Comics was located in 387 Park Avenue South but moved to 10 East 40th Street.

DC Comics

• S.T.A.R. Labs has a location in New York City
• Manhattan Museum of Superhumanity
  

Vertigo Comics

• Fabletown is on Bullfinch Street in Bill Willingham's Fables
• The DMZ is a civil war hot zone in Brian Wood's DMZ