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HashCatalog is a program that can find duplicate files in one or more folders, or between 2 lists of one or more folders. HashCatalog can also create an xml database file containing a listing of files with hashes.
dupliFinder is a app that searches your computer for duplicate files by compairing the MD5 sum of each file. You then have the option of deleting any duplicate files found. Great for collections of MP3s, images etc.. Runs on Windows & Linux with Java 1.5
Synclair is a tool for diff'ing and synchronizing directories. It also includes a utility to find duplicate files (by name, or md5 hash). It is a command line tool, written in Java.