I've been following this thread for a while because my clutch was doing both the chirping when pushed in all the way and occasional shuddering.
I've mentioned it to the Subaru service guys a couple times, they said they couldn't reproduce so nothing came of it.
Well, i went in for the 30k service and brought it up again. This time however i got a call back a couple hours after i dropped the car off, and they asked me if i had noticed that the clutch was a bit heavy. I told them it's been that way as far back as i remember, and that i've mentioned clutch problems in the past.
Anyway, long story short, the tech said there is a known problem with the throwout bearing which had seized in my car. This has caused the clutch to wear unevenly, down to the rivets apparently.
I ended up with a new throwout bearing and whole new clutch assembly (flywheel, pressure plate, etc.); kudos to Subaru for sorting it out under warranty.
The car shifts much more nicely now and no more notchy reverse or chirping clutch, even though it's been pretty cold for the past week or so. Hopefully that's the last of it.