Here are some junk tools other than qaac.
Simple CLI MP4 time code editor. Source and documents are at github, while Win32 binary is at cabinet page. Makefile is provided with the source. You might be able to build this on other platforms (I only tested it to work on Linux).
sudo like command for cygwin, written in Python.
You may want something like this if you are running cygwin on Vista or Windows 7.
Very simple unzipper. Depends on working Python 2.5+ interpreter.
Works like unzip.exe. This one accepts "-e encoding" option to specify filename's character encoding in the zip archive.