This tip was suggested by Jared Thomas:
For /D /R j:\test %%1 IN (*) DO c:\trid_w32\trid "%%1"\* -ae
Replace j:\test with the directory that you want to move recursively through (TrID will not run on the files in the root of this directory).
Replace c:\trid_w32\trid with the path to trid.exe.
Dump the line in a batch file and run.