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• The Dark Knight draws heavily from The Long Halloween and plenty of the Joker's lines are taken straight out of a prose issue collected here. There's also the obvious influence of The Killing Joke and The Man Who Laughs. The Killing Joke was also the primary influence on Tim Burton's Batman.
  
  
• Batman Begins draws from a number of stories include Year One, Blind Justice and The Man Who Falls which is collected here.
  
  
• Captain America: The Winter Soldier was based on the fairly recent Ed Brubaker run which is phenomenal.
  
  
• The Dark Knight Rises combines elements of Knightfall, No Man's Land and The Dark Knight Returns. The Dark Knight Returns is also a major influence on the upcoming Batman V Superman.
  
  
• The Avengers mainly draws from the original first issue of The Avengers, which is collected here and retold again here in a modern setting, as well as The Ultimates. There are plenty of shots that feel like they were lifted right out of The Ultimates. On a side note, Joss also wrote the introduction to the book years ago and it was through doing this that he figured out exactly why the Avengers work.
  
  
• The X-Men movies tend to draw more from the 80's, especially Chris Claremont's run. X-Men 2 draws heavily from Gods Loves, Man Kills. X-Men 3 is loosely based off of The Dark Phoenix Saga as well as Joss Whedon's relatively recent Astonishing X-Men. The Wolverine draws from Chris Claremont and Frank Miller's [Wolverine mini-series] and Days of Future Past is based on, you guessed it, Day of Future Past. Even though X-Men: First Class takes it's name from the comic of the same name it has more in common with the early Stan Lee stuff. X-Men Origins: Wolverine draws from several comics include Wolverine's Origin mini-series and Weapon X. The first X-Men movie isn't really based off any particular arc although it did heavily influence Ultimate X-Men.
  
  
• The upcoming Daredevil TV series seems to be drawing heavily from Frank Miller's run, particularly his origin story The Man Without Fear. While Miller's main run took place in the late 70's/early 80's The Man Without Fear came out in the 90's.
  
  
• Guardians of the Galaxy takes its line-up from the 2004 series but the plot of the movie is all its own.
  
  
• Avenger: Age of Ultron seems to be an original story that's taking it's cues, at least in part, from Ultron Unlimited which is collected here.
  
  
• Man of Steel was heavily influenced by John Byrne's 80's reboot although its structure is heavily modelled on the 2010 graphic novel Earth One. There are also bits and pieces taken from Birthright, Secret Origin and All-Star Superman.
  
  
• Iron Man 3 certainly takes its cues from Extremis but a lot of it is just pure Shane Black. The first Iron Man isn't based on a particular storyline but Tony's origin stuff in Afghanistan is almost identical to the flashbacks in Extremis that revamp Tony's origin for a modern context. Iron Man 2 borrows a little from Demon in a Bottle and Armor Wars but ultimately does its own thing.
  
  
• The writer of the Fantastical Four reboot has mentioned that they've been influenced by Ultimate Fantastic Four.
  
  
• Ant-Man follows an original story but is primarily influenced by the Scott Lang Ant-Man books from the late 70's/early 80's.
  
  
• The Thor movies aren't based on any particular storyline but they are vaguely influenced by Walter Simon's run as well as J. Michael Straczynski's run
  
  
• Green Lantern draws heavily from Geoff John's run, especially his near-perfect origin story Secret Origin
  
  
• AKA Jessica Jones is based on the incredible Alias.
  
  EDIT: Formatting

The Eternity Saga seems to be the consensus "best" Doctor Strange story. If you want to hit the ground running, that's a good a place as any to start:

Collected in Marvel Masterworks Vol 2 - Doctor Strange : http://www.amazon.com/gp/aw/d/0785167706/ref=pd_aw_sims_10?pi=SL500_SY115&simLd=1

Great! There's a few series with the X-Factor title, the one that I talked about it is the second series. It's collected in a couple different sets of trade paperbacks, with X-Factor by Peter David: The Complete Collection Volume 1 probably being the best start. Unfortunately that "complete collection" trade set had poor sales and it only got 2 volumes (probably about half way through that series).

If I recall correctly those two volumes cover some of the biggest dramatic beats though. There's an older series of trades that cover the whole run in smaller volumes (I think about 22 of them?), but I believe it's out of print at the moment.

Pre-order link here

Around $25-30

I'm aware of the story of Wonder Woman's creation and the peculiarities of her creator. I read an entire book about it. I don't see how it's problematic at all these days.