For backpack style Ogio makes really nice bags. For messenger type I think the Tibuk2 are the best. Right now I have a YakPak that is pretty good but I think I might just bite the bullet and spend the $150 on a Timbuk2.
(I know some people will say that $150 on a bag is outrageous but when you carry something every single day for a couple hours a day it is worth getting a good one).
Check out:
http://www.ebags.com/laptop_bag_cent...sub_site_id=52
for some really good deals. I would recommend checking some out in stores though. It's tough to really get a feel for all the pockets and how they will work for you looking at a picture.