Well, this is kind of a long line, and it assumes that you have the gnu or bsd "find", "xargs" and "md5" available on your system as standard utilities (in addition to perl). It could be shorter, but for a few extra characters in the script to use file size together with MD5, you get a lot of extra safety (it's possible to get the same MD5 signature from two files with different contents, but this is far less likely when the files are the same size).

# output of "md5" is one line per file: "MD5 (filename) = signature"

find . -type f -print0 | xargs -0 md5 | 
 perl -ne '/MD5 \((.*)\) = (\S+)/ or next; ($f,$m)=($1,$2); $s=-s $f; 
+if($h{"$m $s"}){unlink $f} $h{"$m $s"}++'
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As suggested by others, you can use the Digest::MD5 module in the perl script (and make the script a bit longer), in case you want to save run time by only computing MD5 signatures on sets of files that are the same size.