The second one is incorrect. The first and third are correct. The third sentence is the correct way to say the second sentence.
February 9, 2012
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If you're talking about keys instead of a single key, the sentences should read as follows:
1) I thought you took them with you.
3) I thought you had them with you.
February 9, 2012
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I think the sentences is ok.
February 9, 2012
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