So the Avengers is a first for movies: a large crossover of individual movies with shared continuities (Freddy vs Jason and Alien vs Predator don't count). Interesting times.
But there's also rumors of sequels planned for movies like Captain America. I don't doubt they will be made, this is Hollywood we're talking about after all. My question is, will they work? Can the individual characters go back to that? What's left to be done with them? If there's a real threat to the world, where will the other heroes be?
In a comic it's easy to have other characters pop their heads in, and there's generally a sense that there's always so much crap going on that all the other heroes are going to be busy anyway. Plus of course time is kind of funny anyway. So you can have Wolverine in his own comic, in the X-Men, and in the New Avengers at the same time. But in a movie it's not so easy to feature other characters, to create that sense of a shared world.
Additionally, you can have a couple of comic story arcs where the protagonist is not challenged on a personal or character level. I'm not just talking about empty 'oh-it's-another-alien-invasion' action, you can tell some very interesting stories in which the protagonist is essentially just an observer, or even has to make difficult decisions without the story centring around him. Take detective shows for example, the stories are about the criminals and victims, and the protagonist is more of a narrative device. While that can be done in a movie, can it be done in a superhero movie?
Lets look at specific examples. For starters, the Hulk. Actually, I think there's a lot of scope for story here since the Hulk is almost the opposite of most heroes: he desperately wants to get rid of his "powers", and there's not much that will change that. In the Ultimates, the comics that the current line of movies most closely resembles in my eyes, Hulk is charged with mass murder and (supposedly) executed. A movie where he flips out and kills some civies, then Bruce has to deal with the guilt while Hulk is back to being a public enemy, but now with other superpowers around to try to bring him in? Could work, especially if you thicken the plot with super-villain meddling (what pushed him to go on a rampage in the first place?). The only barrier I can see is cost: you really want either some other established superheroes or some government-wielded Iron Man tech, or else it will not feel convincing.
Captain America: the whole man-out-of-his-time angle would normally be interesting, but they will have to cover that in Avengers, so it would just feel old if done again. However, it's not just times that have changed, but the politics of the world and of America. Seeing as patriotism is core to his character, it would make sense to deal with patriotism in the modern world. Maybe have him disillusioned with way American government works, perhaps going so far as to create a 'Marvel Civil War' like storyline (if you have the guts), and you might have something very interesting. It's a real challenge to pull off in a shared continuity without either not going far enough to be really interesting or involving all the other players would be a real challenge, and I can't see anyone deciding to take the risk. Perhaps a compromise for a story where his values are challenged by an antagonist who also considers himself a patriot, an anarchist who never the less makes some good points about the need for change, that sometimes to fight for you country means fighting domestic enemies instead of foreign ones. Perhaps Captain America versus the Punisher?
Iron Man: I suppose if you take the plot of the second story, where the government is trying to take his tech and other competitors are catching up, and keep going with it, it could be interesting. Tony Stark suffers a loss of identity when Iron Man armour is deemed a dangerous weapon not suitable for civilian use and he is banned from using it while all around variations are showing up in domestic and foreign military use, then it starts hitting the black market... yeah, you could do something with that, and you wouldn't need any of the other Avengers since this isn't really their business.
Thor: this is a tough one to discuss without knowing more about how he fits in to the Avengers. Is he stranded on Earth? Did he chose to stay? Either way the fish-out-of-water element has been done in the first movie, they'll need something different. I would like to see more of the Asgard / space connection - the change of scenery would make a nice break from the normal city backdrop. The problem is putting Thor in space is too much of a departure from the comics. Perhaps push the mythology angle, with other aliens that inspired different mythologies? In the comics Ares sometimes played the role of Thor's enemy, you could have the Olympians return to Earth with expectations of worship / demands of offering or human sacrifice, or just granting powers to those who worship or sacrifice in their names. Bring in more comic book characters like Ares and Hercules, create a love triangle with Sif and Jane Foster, you could have something.
My point, I suppose, is this is an interesting, perhaps even critical time in cinema. How the Avengers and related movies do could influence what we see for a while. Avengers is a risk, and the hope is that Hollywood will see this as proof that risks can pay off, rather than just a new angle to be exploited and run to the ground. There is scope for the characters to be used in strong stories and good movies, but it will be challenging, and unfortunately I expect the 'franchise' to peter out, run into the ground with mindless sequels, rather than end on a high note or, heaven forbid, continue to grow in quality, variety, and intelligence.