Hi,
I've made a really simple python script to do this. It's far from complete but you can use it as a sample to start something with your students (http://veed.fr/gugodoc/)
Of course, if you need more "power" , your best bet is to choose a more professional solution ;-) I hope you will find something that fits your needs here :
Dammit. Your gugodoc is so close to what I need that the Hacker instinct is taking over and I'm thinking about how I could modify it to give me the rest (e.g. no frames, HTML for the header and footer). However, that's probably just my mind finding another glorious way to procrastinate on my thesis, so I better not.