I recommend that you use sox and wrap it in perl. Sox has a windows binary available.

From the sox README:
SoX (also known as Sound eXchange) translates sound files between different file formats, and optionally applies various sound effects.
SoX is intended as the Swiss Army knife of sound processing tools. It doesn't do anything very well, but sooner or later it comes in very handy.

Sox is also recommended in the TODO section of Audio::MPEG.

If you need more effects than the batch processes that sox provides, you probably need a good UI - use Audacity.