I like Endura Hummvee (sp?) 3/4 length MTB baggies for commuting and if you want they make the same style as pants and shorts. these use a clip in liner so you can wear them with or without padding. My commute is mixed bike/rail and work is casual so I just wear MTB baggies for commuting.
I also got a pair of Zoic convertible pants one time, but my knees were too big. I also sometimes use hiking pants, and rain paints outside for bad weather. Rivendell's MUSA pants would be worth a look too.