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md5deep is a set of programs to compute MD5, SHA-1, SHA-256, Tiger, or Whirlpool message digests on an arbitrary number of files. md5deep is similar to the md5sum program found in the GNU Coreutils package, but has the following additional features:

Recursive operation - md5deep is able to recursive examine an entire directory tree. That is, compute the MD5 for every file in a directory and for every file in every subdirectory.

Comparison mode - md5deep can accept a list of known hashes and compare them to a set of input files. The program can display either those input files that match the list of known hashes or those that do not match. Hashes sets can be drawn from Encase, the National Software Reference Library, iLook Investigator, Hashkeeper, md5sum, BSD md5, and other generic hash generating programs. Users are welcome to add functionality to read other formats too!

Time estimation - md5deep can produce a time estimate when it's processing very large files.
Piecewise hashing - Hash input files in arbitrary sized blocks

File type mode - md5deep can process only files of a certain type, such as regular files, block devices, etc.
hashdeep is a program to compute, match, and audit hashsets. With traditional matching, programs report if an input file matched one in a set of knows or if the input file did not match. It's hard to get a complete sense of the state of the input files compared to the set of knowns. It's possible to have matched files, missing files, files that have moved in the set, and to find new files not in the set. Hashdeep can report all of these conditions. It can even spot hash collisions, when an input file matches a known file in one hash algorithm but not in others. The results are displayed in an audit report.

The hash set audit process was described in the paper Auditing Hash Sets: Lessons Learned from Jurassic Park published in the journal Digital Investigation.

For more details and some examples of using hashdeep, check out the hashdeep getting started guide.