Skyfall and The Dark Knight - both highly successful and considered by many to be the best films in their respected franchises. Both directed by acclaimed directors, featuring iconic hero and fantastic villain.
The very first of similarities I noticed was in the way Silva and the Joker are shown - often surrounded by shadows but usually in the centre of the frame, controlling it, much like they control everything in the movie. Hell, they even use the same disguise at one point, they both bring havoc to the city and they both threaten the person the hero loves.
On close examination, the setting of the characters in the scenes is very similar in these two movies. There are even some characters that have the same purpose. While the villain has many scene stealing moments the hero is presented as brave but flawed and also - very cool. Both films feature killer ride of the protagonist and its destruction which apparently left many in the audience heartbroken.
Next in the series - Breaking Bad and Pulp Fiction