It does seem to vary by store. I went to 3 in the same general area (all within about 45 miles of each other) and only one had any sets on clearance (Pirate Tank, which I bought, Star Destroyer, Temple of Doom, which I should've bought, etc). One of the other 2 did have a clearance tag or two (oddly enough, covering the price tag for the Toy Story Army Men set, though there were none for me to price check to varify) but nothing like the first one.
Peace is a lie, there is only passion. Through passion, I gain strength. Through strength, I gain power. Through power, I gain victory. Through victory, my chains are broken. The Force shall free me.
-The Sith CodeBricklink Store