LaTeX.org

Nate,

This works for me for simple things:
\protected@write\@auxout{}{%
% What's to be written here.
}

Note that you'll want to use the \string macro to defer expansion until when the aux-file is loaded, e.g.
\protected@write\@auxout{}{%
\string\@mycommand{arg}{arg}
}

Hope this helps ...