In the Ultimate Spider-Man cartoon, Spidey already rubs shoulders with Agent Coulson and the rest of the Marvel Universe. But in his live-action movies, he's on his own — because the films are made by Sony, and don't cross over with Marvel's own in-house productions. But that could change.
Over at Forbes, there's a highly speculative and quite possibly crazypants article saying that after Sony puts out Amazing Spider-Man 3 and 4, they'll probably renegotiate with Marvel. And, in a nutshell, Marvel will probably make them an offer too good to refuse, to take Spider-Man back into the Marvel fold so he can appear in future Avengers movies.