Trying out Amazon AWS Glacier with fastglacier.com as the upload GUI app I looked at few SHA256 sum calculating tools, and found this one by Jesse Kornblum to be the best for Windows.
It has some quite useful options like recursive folders calculation, file size limitation, reading file names from file and hash comparing. Be aware it is command-line only.

Update: new versions of the PowerShell have built-in cmdlets Get-FileHash [-Path] [-Algorithm ] to do just that, including sha-256 hash