A large store (superstore) run by a major corporation.
No one knows where the term came from (Because the store's goods are shipped in big boxes? Because the store looks like a big box?) As a result, anyone using the term should be slapped with a large trout for using a phrase which they themselves don't really understand.
In today's financial news, big box store Target is increasing its competition against big box store WalMart. Ow, that trout hurt!