Given the upcoming Agents of Shield TV show, there has been some desire for a return of Agent Coulson. Is there evidence that he canonically died in The Avengers or evidence that this is another one of Nick Fury's manipulations?
Yes. Coulson died.
Joss answered this at the 2014 SXSW. From this article (emphasis mine):
Acknowledging the presence of seemingly-deceased Agent Coulson (Clark Gregg) on the panel – Gregg plays Leonato in the Much Ado ensemble – Whedon tried to explain how the S.H.I.E.L.D. agent returns from the dead.
“I’ll tell you guys this, Heimlich,” Whedon joked, before effectively clamming up about the show. “I can’t talk about it,” he admitted, but said that he did bring Coulson back from the dead for the ABC drama. “Yes. For realsies.”
Within the TV show
Agent Hill says that Coulson died for 8 seconds (though he claims 40) and that Fury faked a full death to unite the Avengers. Coulson was sent to recover in Tahiti.
A short exchange between Agent Hill and
Shepherd BookDr. Streiten leads viewers to believe that there is still more to Coulson's "death" and "recovery" than Coulson or the viewer knows.
In Season 1, Episode 3: (The Asset)
A major point is made to demonstrate that Coulson has lost what should have been instinctive muscle memory when he is unable to take apart and reassemble a gun as quick as he normally could pre-impalement.
In Season 1, Episode 11: (A Magical Place)
Dr. Streitan explains that Coulson had been dead for days and that his memories had been altered. After being revived (by some still unknown means), his memories are altered to restore him to something closer to his original pre-death personality.
Within the movies
It's worth noting that while Coulson has been revived, and is alive and kicking in the Marvel Cinematic Universe, Whedon still considers him dead for the purposes of the movies, explaining why he hasn't shown up in any of the MCU movies since his trip to TAHITI.
A lot of people come back in The Winter Soldier. It’s a grand Marvel tradition. Bucky was supposed to die. And the Coulson thing was, I think, a little anomalous just because that really came from the television division, which is sort of considered to be its own subsection of the Marvel universe. As far as the fiction of the movies, Coulson is dead.
However, since Whedon has stepped back from his position as one of the primary forces in the MCU creative team, The Powers That Be™ may change this.
Actually in the marvels agents of shield tv show coulson is revived by Fury using alien blood. Coulson belived he died for 40 seconds but nick revealed it was over a week. So Coulson didn’t accept that he was put through all of that pain just to come back to life and he just wanted to die. He also started writing alien symbols on to the wall which is later revealed to be a city