How can I generate an MD5 sum for a folder on Windows?

If you want to use a GUI, I can recommend Fsum Frontend.

Fsum Frontend is a free and easy-to-use tool that allows to compute message digests, checksums and HMACs for files and text strings. It supports drag-and-drop and you can handle multiple files at once. The checksum generated can be used to verify the integrity of the files.

It supports 96 algorithms: [...] md5 [...]

Screenshot of FsumFrontend

As the name implies, Fsum Frontend is a GUI for (among others) SlavaSoft fsum.

A fast and handy command line utility for file integrity verification. It offers a choice of 13 of the most popular hash and checksum functions for file message digest and checksum calculation.

Its features include:

  • Possibility to act recursively. FSUM can operate not only on files from a specific directory, but also on files from all subdirectories of the specified directory;
  • Work with large size files. (Tested on file sizes of up to 15 GB);
  • Full compatibility with md5sum utility

Screenshot of fsum.exe command line usage

You can achieve the equivalent to your Unix command (minus the sorting) with the following:

for /R . %f in (*.*) do @certutil -hashfile "%f" MD5

You can change the dot (.) for whatever folder you want to recurse from, and the *.* to whatever file mask you need in order to narrow down your file set.

PowerShell provides loop statement, some people may prefer this syntax

foreach($f in dir){ certutil -hashfile "$f" md5}