Are the lore associated with Knights of the Old Republic (and soon to be released Old Republic) video game considered as Star Wars canon?
According to this answer, I believe that SW: KOTOR and the sequel are considered C-level canon. It is canon unless it contradicts something that is in a novel or in G-level canon.
In any SW video game with multiple endings to quests, I believe that the canon resolution is the 'best' one - the one that offers the most 'light side' points. In canon, I believe that all side quests are considered to be taken.
It's also worth pointing out that video games are typically considered 'less canon' than the EU novels - G-level trumps novels, novels trump video games. Comics most likely fall in with novels, except when they're tied to a game - then the comic trumps gameplay, but an EU novel still trumps it.