I have commuted with laptops for a few years, but it's not an everyday thing... just as needed. First I did this with a messenger bag that had a laptop sleeve. There are many options in this category, but this can be a heavy and sweaty experience depending on the laptop's weight and your commute. I prefer panniers, and decided to buy a laptop pannier a couple of years ago. Carradice and Arkel both make panniers with laptop sleeves.
I would take a look at the following commuter pannier from Arkel... it looks really nice:
http://www.arkel-od.com/panniers/com...asp?fl=1&site=
I have the Arkel Briefcase, which is a really nice bag...but is kind of heavy. It weighs over 4 pounds and I can't figure out where that weight is coming from. Arkel's other urban panniers, like the Commuter, weigh half as much and offer more capacity. I also have the Arkel Utility Bag... their stuff is expensive, but really excellent in terms of design and construction.
So carrying a laptop is no big deal... you just have to decide what type of bag you want. Messenger bags and backpacks both come in configurations for laptops. Then there are briefcase panniers and commuter panniers with laptop sleeves.
Another factor is the size/weight of your laptop. If you have a 17" laptop your options will be more limited. If your laptop is heavy, I'd definitely consider the pannier.
Sean