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I'm assuming this is a New Beetle (which started production in 1998)?
I'm guessing that you may have an issue with your catalytic converter, which will rattle when starting, and under certain load conditions, and sometimes over bumps. You can also try smacking the catalytic converter with a block of wood or a rubber mallet and see if it rattles.
They are covered by an 8 year 80k mile warranty, so you are well out of that now. They can be around $800 from the dealer.