My commute is 7 miles each way, so I wear gym clothes. In the winter, this is a base layer topped with a t-shirt and running pants with tights underneath. In the summer, it's gym shorts and a light-weight and/or sweat-wicking t-shirt.

When I get to work, I cool down for about 15 minutes and then change into my work clothes (business casual). Except on the hotter summer days, smell isn't an issue. On those days, I bring along an unscented wipe in a plastic bag and wipe down the more stinky body parts. A change of underwear helps, too.