I'm surprised nobody has commented on this yet -- in the Day 1 Telltale video from the San Diego ComiCon that's up on the blog page, Bill Willingham states that the Fables game storylines will be "in canon."
That seems pretty rare for game adaptations -- Telltale has been very good at coming up with stories that fit into existing universes without impacting them in any significant way. To have Willingham onboard with treating this story/these stories as canon may allow for some more interesting and/or significant developments.
The closest example I can think of in adventure/comic book games would be the Scott Adams QuestProbe series done with Marvel in the mid-80s -- but even there the Chief Examiner seemed to get retconned a bit as the series went on, shifting from (I maintain) Scott Adams himself in the first game to being a more generic character by the third. The fourth game was never published but the tie-in story did appear in a Marvel comic book later on, so I think it counts as canon (to the degree anything can in the ever-mutable world of superhero comics.)
Maybe the Fables universe just has so many story possibilities that Mr. Willingham feels comfortable calling the game canon without feeling like it will limit him. But I'd like to think it's a vote of confidence and trust in Telltale's ability to treat his world and characters with integrity and honesty. It's an interesting development, anyway.