Strictly speaking, only the the first sentence is unambiguously correct:
I can find the tool neither in the kitchen nor in the bathroom.
But what's intriguing to me is the third sentence in which a comma has been introduced. Without that comma, the sentence is unequivocally wrong. But a comma can be used to separate two independent clauses. Combine that with the concept of elision, and the third sentence could actually be interpreted as:
I cannot find the tool, it is neither in the kitchen nor in the bathroom.
I dislike that punctuation and I would either use a semicolon or make it two sentences. But if the sentence is interpreted that way then it only has a minor punctuation issue, while the use of 'neither' and 'nor' is actually correct.
I cannot find the tool, neither in the kitchen nor in the bathroomandI cannot find the tool, either in the kitchen or in the bathroomsound fine and mean the same thing to me (though the former sounds a little more formal). Not sure if a prescriptivist would differ, though. – grautur Jun 17 '11 at 05:48