I use water-resistant LL Bean Gore-Tex pants over my work clothing (suit and tie). I'd strongly advise breathable, water-resistant fabrics rather than the fully waterproof ones. In particular, the plastic coated things will turn you into a mobile sauna until the coating wears through, at which point the rain protection ceases. I've been doing a 5.5 mile year round commute for seven years, and the LL Bean pants have proven very effective.

Unless it is cold, I avoid wearing rain gear unless it is actually raining. Decent fenders to protect against road splash are a must. It is also good to have a rack and/or panniers top carry the rain gear when you don't need it.

Paul