If you're running on Windows and want a quick and dirty solution, you can use BATPROC to launch n number of jobs for logparser. Logparser has a has function (HASHMD5_FILE). You can use any hashing tool in place of logparser.
You can also utilize Powershell, create an MD5 function (or use the Powershell Community Cmdlets), and then use it's background Jobs function to multithread the script. I a "multithreaded" Powershell script to collect audits from all our workstations.
As for an all-in-one-not-a-script solution, I haven't run across any that I've personally tried. I rarely have to hash a bunch of data, so trying to find a tool that's multithreaded wasn't a priority 😛
Though like jrjiri, I'm curious as to what you or others come up with.