Simian (Similarity Analyser) identifies DuplicatedCode in Java, C#, C, CPP, COBOL, JSP, HTML source code and even plain text files. It costs money.

Runs under any Java2 1.3 or higher virtual machine

See 
*** http://www.redhillconsulting.com.au/products/simian ( BrokenLink )

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This is one of many tools for finding code duplication.  For others (some free), see CategoryDuplicationFindingTool.