It all started with Iron Man, with a mysterious agent called Agent Coulson trying to debrief Tony Stark about his incident, then a cameo after the credits from Nick Fury that he wants to talk to him about The Avenger Initiative. Finally in Iron Man 2, he becomes a consultant, so now he is part of the team alongside Nick Fury, Agent Coulson, Black Widow and Hawkeye. There are still three character to join, Hulk, Thor, Captain America.
We all know that at the end of Captain America he gets debriefed by Nick Fury as shown by the leaked photos a few weeks ago, so thats him in the team. Still Hulk and Thor left.
Obviously in The Incredible Hulk, Bruce Banner doesn't even get approached by Nick Fury or Agent Coulson because he is on the run and S.H.I.E.L.D are helping the U.S Army and General Ross to find him. But at the end, Tony Stark as a consultant approaches General Ross about an unusual problem (Hulk) and that he is putting a team together. So it looks like Hulk will be the villain at the beginning of The Avengers, then after getting defeated, he gets asked to join the team to fight a bigger threat (please be skrulls!!!).
But in Thor it's a different story, in the scene were Thor defeats The Destroyer and Agent Coulson approaches him and says "Donald, I don't think you've been completely honest with me", Thor says "You and I, we fight for the same cause, the protection of this world (Skrulls lead up?), from this day forward you can count me as your ally if you return the items you have taken from Jane". Then when Thor flies up in the air with Jane, Coulson shouts "Wait, I need to debrief you" (Like Coulson trying to debrief Stark).
I like the way the film handled Thor joining the team rather than Coulson asking him because that could be silly, but instead Thor says he will fight for the safety of this world because of Loki and the Destroyer incident. In The Avengers, Coulson will probably need him because of Loki (again) and this bigger threat (I still think it should be the Skrulls).