Some spoilers follow:
As everyone whose seen The Avengers and had the good sense to stay a while longer after the initial credits should know, Thanos will be the next villain in the film franchise. Thanos was an alien called The Mad Titan in the comics and sought the destructive power of a mystical device called the Infinity Gauntlet, a weapon briefly seen in the Asgardian weapons chamber in Thor. We will most likely see his power-hungry quest for the Gauntlet as the Avengers try to stop him. Along with Thanos comes the rest of the Shitari, the aliens from the first film, which hints at yet another alien invasion.
The Ant-Man film has been officially announced and is currently in pre-production. Its expected release is before the Avengers sequel. This assumes the Ant-Man film will introduce its title hero: Hank Pym along with his wife Janet Pym, the Wasp (two of the original team members from the comics). If the movie is a hit there is no doubt the two characters will be integrated into Avengers 2 to join the original cast of heroes and possibly more additions.
The three main heroes of the Avengers are announced to have sequels of their own and are already in production of some of them. These movies, however, are not meant to continue from the Avengers directly. Each film’s storyline does take place shortly after the events of the Avengers, but will focus solely on the individual hero. This will give a chance for the creators and writers to explore the heroes outside of the team-up atmosphere and frees the films from having continuity between them, something that was needed in their first films.
In an alternate ending to the first film, viewable in the special features, shows us Maria Hill meeting the council on her own. The scene suggests she has taken the role of acting head of SHIELD away from Nick Fury (a story choice made in recent comics). Seeing as how Hill was not too fond of the Avengers Initiative in the first place, who knows how this change of management with SHIELD will affect their relation with the team in the sequel.