The current version of MusicBrainz Picard uses audio fingerprinting. It is primarily a tagger, so be sure to disable it's automatic tag update feature when using it to only find dupes.
From a recent review:
"MusicBrainz Picardis a cross-platform music tagger that is using an album-oriented approach when it comes to tagging files. What many users will like is the fact that it can do so almost automatically. All you basically need to do is point it to a directory with music, and the program will scan and attempt to match up the files automatically. While this may work well for some of the music, you may notice that there are still unmatched entries left in the program’s left column after the initial scan.
Once you realize that, you can make use of the program’s lookup or scan modes to identify the remaining songs. If you select lookup, Picard will connect to the Internet to match each song to an artist and album. If that succeeds, it is moved to the matched listing on the right where you find a list of properly identified albums along with the song count for each.
The lookup takes quite some time but appears to be very thorough in this regard. Only 300 of the 3700 music files that I had added to the program were identified during the initial scan. The lookup took an hour to complete, and I ended up with 469 files that the program could not look up online.
The functionality that Picard provides does not stop here though, as you can then use audio fingerprinting
to identify the remaining tracks. Before you can use that function, you need to configure it in the options. Picard supports two different audio fingerprinting solutions
and I’d recommend you run both if the first does not identify all of the remaining songs."