TOR doesn't seem remotely canon to me, anything with that many players making that many different decisions can't be canon.
TOR has the canon established by the novels set before the game. There will undoubtedly be a canon storyline as well, one that's potentially an amalgamation of parts of each class story. SWG had canon parts as well, so it wouldn't be a surprise at all.
Anything that hasn't got an infinities label on it, pretty much... > http://starwars.wikia.com/wiki/Canon Skip to the 'Canon in the Holocron Continuity Database' and read on from there.
I think it's safe for now . . . until Disney finishes the ST that is. I am hoping and suspecting they will start a new series set during the time of the Old Republic so they can have mega Sith v Jedi action.