Yes. Thanos is in The Avengers movie.
Not a big surprise for those who have been following the various rumors as the name of Thanos has popped up on more than one occasion.
From what I gather, Thanos is either mentioned or hinted at in the beginning of The Avengers movie, and then featured in a mid-credit scene, with possibly Annihilus.
Apparently, the post-credit scene for The Avengers was filmed after its world premiere.
Now with Thanos present in the movie, just what does it mean for Marvel Studios?
Well, we do know that Marvel Studios likes to include extra scenes that involve their future movies. Nick Fury was in the post-credit scene of Iron Man; Tony Stark was featured in The Incredible Hulk; Loki, Fury, Selvig and the Tesseract (Cosmic Cube) in Thor, and of course the post-credits scene of Captain America began The Avengers.
The current thought is that Marvel Studios will feature Thanos as the villain in The Avengers 2.
So how will it fit?
In comic book continuity, Thanos was brought down by The Avengers and Captain Marvel while he was in possession of the Cosmic Cube (Tesseract). His having failed to acquire the Cosmic Cube led to his search for the Infinity Gems in order to get back in good graces with Mistress Death. Interestingly enough, prior to that, Thanos was known for using alien races to wage his war of death and destruction.
If what is being said about Thanos in The Avengers movie is correct, Thanos gave some of those alien forces to Loki, in some kind of exchange — possibly for the Cosmic Cube, or the Infinity Gauntlet (just the "glove" part). Apparently, the mid-credit scene involved "Annihilus" telling Thanos that Loki had failed in acquiring the Cosmic Cube, but Thanos turned and smiled — as if that was all part of the plan; meaning Thanos' true goal is the Infinity Gems.
And it has been said Thanos was shown with a green gem as well.
So we see that Marvel Studios has chosen to "bypass" the "Captain Marvel vs. Thanos battle for the Cosmic Cube (Tesseract)" storyline, which still ends with the same result — the Thanos quest for the Infinity Gems.
However, before we get to the Infinity Gems, Thanos actually built a "Synthetic Gem" that was made up of the power of the other gems. And it was green.
Thanos had acquired five of the six Infinity Gems, with the sixth belonging to Adam Warlock. In a previous battle against Warlock's evil self, The Magus, Thanos had siphoned off Warlock's soul gem which he then used to create a "Synthetic Gem."
Thanos then goes on to use the Synthetic Gem in an attempt to destroy the stars of the Universe. The Mad Titan sends an alien armada, against the Earth and The Avengers, in an attempt to distract The Assemblers, as the Avengers, and most notably Iron Man, have previously thwarted Thanos' evil plans before.
Now, the green gem Thanos was seen with in The Avengers movie just might be the "Synthetic Gem," as the actual green Infinity Gem - the Soul Gem - belongs to Adam Warlock. In The Avengers movie, Thanos would then use the Synthetic Gem to aid Loki, and again, we see Marvel Studios "bypassing" the Synthetic Gem storyline, but the end result is still the same.
Or, another possibility is that Thanos is in possession of an Infinity Gem and used Loki as a distraction to discover the location of another Infinity Gem located on Earth. This scenario is actually less complicated, with the end result still being the same — Thanos seeking the Infinity Gems.
Enter The Guardians of the Galaxy.
We know a Guardians of the Galaxy movie is in development, and it will feature the most current comic book roster, of which included — Adam Warlock. The Guardians of the Galaxy movie looks to be in theaters around 2014 or 2015 at the latest. The Avengers 2 looks to be around 2015 or 2016 at the latest. Regardless, I think their release dates are too close to go from The Avengers to Guardians of the Galaxy to The Avengers 2.
What I think might happen is that Thanos will be the featured villain of The Avengers 3, with Annihilus the villain of the Guardians of the Galaxy movie — referencing Annihilation. In the Guardians of the Galaxy movie, Annihilus might attempt to get hold of Warlock's Soul Gem for Thanos, which leads to The Avengers 3. Or the Guardians might be come together to stop Thanos and Annihilus' invasion from the Negative Zone.
[[wysiwyg_imageupload:1445:]]To boot, the Doctor Strange and Inhumans movies could fit in rather nicely prior to The Avengers 2 (or after) as both could involve the Infinity Gems just as well. In the comic books, Thanos found a gem on the moon — the home of the Inhumans, and Doctor Strange is currently in possession of an Infinity gem — the soul gem, I believe.
Regarding The Avengers 2, I would expect the upcoming post-credit scenes in the sequels of Iron Man 3, Thor 2, and Captain America 2 to be setting up that movie, with most likely Ultron as the villain, or some such classic "Avengers" villain.
Now that my speculation is near complete, getting back to Thanos, it must be noted that The Avengers have always had help in the form of some Cosmic Do-Gooders (Captain Marvel, Adam Warlock, Moondragon, Gamora) to defeat Thanos.
As many have mentioned, The Avengers alone are not enough to withstand the power that is Thanos.
We've seen Thanos, but yet to see the Cosmic Assemblers.
For a quick recap on the history of Thanos, I suggest you hunt down a copy of Avengers Annual #7 (1977) — an awesome cosmic display by Jim Starlin!