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In my neck of the woods I've found Meijer to have the best clearances. Wal-Mart is always hit or miss for me, and Toys R Us has such high markups to begin with their clearance sales aren't often all that great of value.
Although I don't recall the details, there is a certain 'foolproof' formula based on a minimum per-piece cost that a Bricklinker parts guy I know uses when purchasing sets at clearance prices.