Personally I wear bike shorts and a wicking shirt but I have easy access to a shower at work and I like to push it on my commute. Many people successfully ride in whatever they're going to wear at the office.

As far as SPD pedals go, it's an open question as to whether you'll see much benefit from them during a commute. Personally I like them and have experienced the competitive advantages but as far as making your commutes faster... well, I don't see a lot of difference overall. If you have some significant hills to deal with that may tip the scales more in their favor.

If you already have them and are comfortable with them, then by all means use them. Having some sort of foot retention can be nice in wet weather and it makes bunny hopping easier, though some would call it cheating. The downside of course to SPDs is the expense and having to wear compatible shoes. Mine are pretty comfy and I can wear them anywhere but they do click on any concrete that isn't really smooth.

edit: Something else I thought of regarding clipless pedals (or any foot retention). Even though it doesn't make much difference in terms of my overall commute time, the extra acceleration and ability to hold a pace longer does come in handy now and then. This might actually make up for those times that I still inexplicably have trouble clipping in