cscript.exe c:\path\to\wmcmd.vbs -loadprofile encoding-profile.prx -input "F:\input-folder" -output "F:\output-folder"
This page explains how to get the prx files from the WMEncoder, Properties -> Compression -> Edit -> Export button. But of course, it did not work for me,
.Error occurred in transcoding: Error Code = 0xC00D002F
since my WME does not work with Xvid encoded files, needs a nominal crop of a couple of pixels before it works. Probably then it uses a different input codec or whatever.
But checking out
cscript.exe wmcmd.vbs /?found that it supports WMEncode wme session files too! So next time I can try that.
Virtualdubmod also has a batch encoding option with input and output folders, as given at this page and I used it this time: File -> Job Control, and Edit -> Process Directory from the Job control window.