I'm not exactly sure how you want to carry it, or how much protection you desire (aluminum hard case, etc.), but check this out:
I already have a backpack and I do not want to carry a briefcase or laptop bag with a backpack. So, I put a cover on my laptop and accessories and throw them into my backpack as well. It's not designed for a laptop (JanSport), but it is one of those ergonomic backpacks with sufficient padding on the bottom and the back. I still have room for 3-4 books in the back compartment, 2 front compartments and lots of side pockets, etc. Works out well. I've been carrying laptops like this for almost 5 years now. Not a single ding, scratch, crack, whatever.
Here's the cover:http://www.sonystyle.com/is-bin/INTE..._NotebookCases
Just trying to help,