<p>I know this an old thread, but every so often I look around for raw averaging tools and this thread continues to be one of the top links every time.<br>
So for those that come here looking I just wanted to say that there IS software to do something like this, Pixel Fixer at pixelfixer.org . It does median and maximum and also dark frame subtraction with raw files outputting raw files (among other tools). He hasn't added average but given a poke I think he would.</p>