I've got a couple of books that mention commuting, how to incorporate a commute into a training plan, and also how a commute can interfere with a training plan. Some of the Burke books mention commuting, and I think the Base Building for Cyclists book does too. I'm currently reading through Training Plans for Cyclists which is fairly recent (2009 pub date) and has a nice chapter on nutrition and vitamin / mineral supplements, also has a variety of plans for various goals that you could probably incorporate your commute into. .

One thing I've read by some commuters is to save the hard longer intensity rides for the ride home instead of on the ride in to work. Easy mellow ride in, then crank out a longer ride home for the training aspect.

I'm no expert, I just like to ride.