My advisor (Voicu Popescu) wrote a couple of nice materials about "How to Write a CS Paper". The emphasis is mostly on how to do it in the computer graphics field, but perhaps it's applicable to other CS domains too:

In prose form: http://webarchiv.ethz.ch/digitalartweeks/web/uploads/DAWIntr...

In slide form: http://spaf.cerias.purdue.edu/classes/Popescu.pdf