Technically, the crate itself isn't a weapon; that would be the pies inside it. Yes, you're reading this correctly: Jellybob uses pies as weapons.
The concept was mostly inspired by the weapons from Donkey Kong 64. Jellybob can pick up single pies lying around, or snag entire crates with several of the things.
Throwing pies is a key long-range attack. Jellybob's other offensive moves are melee-based, so the pies can be rather useful in a pinch.
I should also point out that there should also be a melee attack you can do with the pies, which is triggered by hitting the whatever "throw pie" button when really close to a baddie. Jellybob will draw out two pies and clap them together for a more powerful attack. It only counts as one pie in his inventory, though. Don't ask me how this works. I don't think he even knows.