With a bit of creative batch file work.
This needs Windows 2000, XP, or 2003 to work. It might work on Windows NT, but won't work on 95/98/ME.
Pull up a command prompt and change to the directory containing mo3enc.exe. Then type the following, replacing #root# with the root directory of the modules (e.g. D:\stuff\modules - remember to use quotes " if the path contains spaces!), and #options# with any options for mo3enc.exe.
FOR /R #root# %I IN (*.it *.mod *.s3m *.xm) DO mo3enc.exe #options# "%~fI"
That's it! That will recursively iterate through every file and folder in #root#, and run mo3enc on any .it/.mod/.s3m/.xm files in there. It *won't* work if the files are compressed with a third-party program (e.g. winzip or winrar).
(if you're ever bored, type "FOR /?" at a command prompt. You'll be suprised at what it can do)