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 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.
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 best place to start with modern Thor is the relaunch by J. Michael Stracynski. Thor's had fairly consistently good writing for the past seven years, starting with JMS, then Kieron Gillen, then Matt Fraction.
And if you need to fill in the gaps for Siege, you should totally read the JMS run of Thor too 'cause it was pretty awesome. That's what I love about comics, all the interconnecting stories.
If you haven't already, you should read J. Michael Straczynski's run of Thor and Thor's tie in to Siege (which is the best part considering it is the Siege of Asgard). Doom is a bit extreme in those. At least in the Siege part.
So, the Ragnarok storyline and what leads up to it is generally not very well received. I personally haven't read it, but don't hear great things.
However, all of the work on Thor since then has been fairly outstanding.
The story that brought Thor back to comics was done by JMS. The writing is fairly good, but the artwork is some of the best Marvel has ever done and it makes it almost a must read. Kieron Gillen then continues these story arcs for a bit up until the "Siege" crossover event which features Norman Osborn's HAMMER going up against the Avengers at Asgard. I personally like Gillen's writing more but the artwork isn't quite as strong. It's still good, put Olivier Copiel's artwork is close to flawless so it's hard to compare.
After this, Matt Fraction came in for a bit. Honestly? The arc is underwhelming. It's very possible to skip this.
After this, Jason Aaron came in and is still working on this title right now. I think his first arc is a must read for any Thor fan.
So if you're really looking to dive into Thor, I would probably start with the JMS arc that is immediately post Ragnarok. If you want to get into the current Thor story and skip some of the other material, you can jump to Jason Aaron's run. Here are the links for amazon.
The hardest ones to get into are the X-Men books, because their stories are so twisting and turning and there's a god damned crossover every six issues. So the following TPBs are listed from most recent to furthest back. If you pick up all of them, you will be sufficiently abreast of the current details in the X-Men's lives, but you can probably get a general idea if you just pick up the latest one or two.
X-Men Trade Paperbacks:
Second Coming
Nation X
Messiah War
Messiah Complex
House of M
Also, if you want just GOOD X-Men stories that aren't particularly tied down by tie-ins and crossovers, pick up any of the "Astonishing X-Men" trades.
To know what's going on in the rest of the Marvel Universe (with the Avengers and whatnot) read some of these, again, listed most recent to further back:
Marvel Big Event Books:
Siege
Dark Reign
Secret Invasion
World War Hulk
Planet Hulk
Civil War
There are, of course, nine million spinoff books, but if you pick up the main books, they're generally able to tell the whole story.
Other Great, Non-Crossover-Gold-Foil-Craziness Books from Marvel:
Old Man Logan
Runaways
Iron Man: Extremis
Immortal Iron Fist
Thor (the reboot, by J. Michael Straczynski)
Secret Warriors
Anything from the Ultimate Line...
Creator-Owned Stuff That's Amazing:
Invincible - Robert Kirkman
Powers - Brian Michael Bendis
Fables - Bill Willingham
Y - The Last Man - Brian K Vaughan
Sandman - Neil Gaiman
Lucifer (Sandman Spin-Off) - Mike Carey
The Unwritten - Mike Carey
Crossing Midnight - Mike Carey
DMZ - Brian Wood
Northlanders - Brian Wood
Mice Templar - Michael Oeming
Kick-Ass - Mark Millar
Chosen - Mark Millar
Wanted - Mark Millar
Scalped - Jason Aaron
The Boys - Garth Ennis
The Sword - The Luna Brothers
Girls - The Luna Brothers
Ultra - The Luna Brothers
Wasteland - Anthony Johnston
NOW! That's like... $500 worth of trade paperbacks right there, if not more. Please don't try to buy all of those tomorrow.
But, those are some ideas of books that will be a good read. If I had to give you a top three list of TPBs to go out and buy tomorrow:
Sentry is pretty instable mentally, so he's not very reliable. Osbourne manages to get him on the dark Avengers though. If you read Siege event, Sentry and Ares fight. Ot does not end well for one of them in a very wtf moment that caught me by surprise.
The Thor run vol 1-3 starting with 1 linked below is a great read. This shows Thor coming back after being gone for a while from Ragnorok (Thor disassembled). Definitely good to read this before Siege. I read those and dark Avengers Siege prelude and was very satisfied.
Just a preference. Look up a brief synopsis (links included), see which costumes/power sets you like more, etc. Here are some recommendations:
Aquaman
Black Panther
Thor
Wonder Woman
EDIT: Formatting
Here's the book it came from. Really good art and characters and it really impacted the all the Thor stories to follow it.
For more really awesome Thor try[ this one.] (http://www.amazon.com/Thor-Thunder-Volume-Butcher-Graphic/dp/0785166971/ref=sr_1_1?ie=UTF8&qid=1414265207&sr=8-1&keywords=thor+god+of+thunder) Thor has to fight a serial killer who hunts Gods with beautiful watercolory art. Here's some really touching screencap from that series.
Oh and stop by /r/comicbooks sometime, we love getting people into comics.
The best place to start with modern Thor is the relaunch by J. Michael Stracynski. Thor's had fairly consistently good writing for the past seven years, starting with JMS, then Kieron Gillen, then Matt Fraction.
Here's a reading list:
Once you've read through that, you might want to read Gillen's Journey Into Mystery, which stars Loki and also features Thor a bit.
I got this.
Assorted Spin-Offs:
Odds & Ends:
In order:
Civil War
Secret Invasion Optional since it doesn't really involve Cap, but it sets up the fall of Shield and how Osborne forms Hammer
Siege
And if you need to fill in the gaps for Siege, you should totally read the JMS run of Thor too 'cause it was pretty awesome. That's what I love about comics, all the interconnecting stories.
If you haven't already, you should read J. Michael Straczynski's run of Thor and Thor's tie in to Siege (which is the best part considering it is the Siege of Asgard). Doom is a bit extreme in those. At least in the Siege part.
Thor Vol. 1
Thor Vol. 2
Thor Vol. 3
Thor by Kieron Gillen
Siege
Also The Incredible Hulk vol. 1 by Jason Aaron has a pretty cool appearance by Doom.
So, the Ragnarok storyline and what leads up to it is generally not very well received. I personally haven't read it, but don't hear great things.
However, all of the work on Thor since then has been fairly outstanding.
The story that brought Thor back to comics was done by JMS. The writing is fairly good, but the artwork is some of the best Marvel has ever done and it makes it almost a must read. Kieron Gillen then continues these story arcs for a bit up until the "Siege" crossover event which features Norman Osborn's HAMMER going up against the Avengers at Asgard. I personally like Gillen's writing more but the artwork isn't quite as strong. It's still good, put Olivier Copiel's artwork is close to flawless so it's hard to compare.
After this, Matt Fraction came in for a bit. Honestly? The arc is underwhelming. It's very possible to skip this.
After this, Jason Aaron came in and is still working on this title right now. I think his first arc is a must read for any Thor fan.
So if you're really looking to dive into Thor, I would probably start with the JMS arc that is immediately post Ragnarok. If you want to get into the current Thor story and skip some of the other material, you can jump to Jason Aaron's run. Here are the links for amazon.
http://www.amazon.com/Thor-Vol-J-Michael-Straczynski/dp/0785117229
http://www.amazon.com/Thor-God-Thunder-Vol-Butcher/dp/0785168427
The hardest ones to get into are the X-Men books, because their stories are so twisting and turning and there's a god damned crossover every six issues. So the following TPBs are listed from most recent to furthest back. If you pick up all of them, you will be sufficiently abreast of the current details in the X-Men's lives, but you can probably get a general idea if you just pick up the latest one or two.
X-Men Trade Paperbacks:
Also, if you want just GOOD X-Men stories that aren't particularly tied down by tie-ins and crossovers, pick up any of the "Astonishing X-Men" trades.
To know what's going on in the rest of the Marvel Universe (with the Avengers and whatnot) read some of these, again, listed most recent to further back:
Marvel Big Event Books:
There are, of course, nine million spinoff books, but if you pick up the main books, they're generally able to tell the whole story.
Other Great, Non-Crossover-Gold-Foil-Craziness Books from Marvel:
Creator-Owned Stuff That's Amazing:
NOW! That's like... $500 worth of trade paperbacks right there, if not more. Please don't try to buy all of those tomorrow.
But, those are some ideas of books that will be a good read. If I had to give you a top three list of TPBs to go out and buy tomorrow:
I really enjoyed JMS's run on Thor. The art by Olivier Coipel is great. It leads into the Siege event which is pretty cool too.
Sentry is pretty instable mentally, so he's not very reliable. Osbourne manages to get him on the dark Avengers though. If you read Siege event, Sentry and Ares fight. Ot does not end well for one of them in a very wtf moment that caught me by surprise.
The Thor run vol 1-3 starting with 1 linked below is a great read. This shows Thor coming back after being gone for a while from Ragnorok (Thor disassembled). Definitely good to read this before Siege. I read those and dark Avengers Siege prelude and was very satisfied.
https://www.amazon.com/Thor-Vol-J-Michael-Straczynski/dp/0785117229
I'm quite partial to the J.M.S. run of Thor which is a few years old!
Thor J.M.S. Omnibus
or start here if you want to go the easiest route!
Thor Vol 1
Thor Vol 2
Thor Vol 3
I started with Straczynski's run, which picks up after the events of Ragnorok and the Civil War.