Canon is the two games (FS1 and FS2) including all mission briefings, tech room specs, cutscenes, and table entries, the expansion pack (Silent Threat, original), multiplayer campaign for FS2 (Operation Templar), and the Freespace Reference Bible, in that order. The only other thing that qualifies as canon are statements made by the developers, but as the original text of most of that has gone the way of the dodo, those can't be completely relied on.
Eventually, the Wiki will have it all laid out for you in a nice, readable form. Until then, you'll have to hunt and peck your way through.