Well, they're not doing a blanket cut, but they're cutting back.
I would expect the first things to go will be anything that contradicts the stories for the new films. Stuff pre-Ep 1 will stand a far better chance of being canonized than the rest, the earlier in the timeline the better probably.
I'd be surprised if the Old Republic stuff (the stuff core to the games, Revan etc, not necessarily the novels written around that) got the axe. Even if the force powers were a bit nuts the games did very well and there was lore-wise a mass wipeout of force users to 'reset' it back to film levels if I recall, it also gives explanation as to the "always two" rule that Yoda refers to about the Sith in Ep1. Force Unleashed game is probably the one most likely for the chop out of that type of material, as the powers were a bit OTT.
EDIT: I wonder about the Clone War's TV series... I'd imagine it will stay canon, but you never know.