I can't believe STM is so popular, because in all the other "bag" threads, they rarely come up this often. I have an STM bag for my 12" PB (the "Small Loft" shoulder bag), and it isn't bad. The padding used isn't as thick as it could be, but it's still on par with the Crumpler bags.
Let me tell you something about most of the protection that these bags offer: it's almost all the same. People talk about Crumpler bags or STM. Guess what? Feel the padding of their shoulder bags, and you'll notice right away that one doesn't have more or less padding than the other. Sometimes it matters, but not really for laptop bags. For example, I bought a Lowepro bag for my dSLR camera because the padding was clearly thicker. With most bags from companies dedicated to making laptop bags, it's almost the same.
The big difference between bags, IMO, is how well the laptop fits in the padded pocket, and the compartmentalisation offered in the bags. Some don't have enough pockets to store all your stuff, and depending on where the pockets are, they can actually offer protection to your laptop if you're keeping stuff in those pockets. In this way, backpacks are usually better, but much bigger than shoulder bags.
My STM is good, but buying the equivalent Crumpler bag will cost you more money. Why? Because they're way too popular right now, and that's going to cost you money. If you have the money though, buy what you like. However, I can tell you for certain that for most shoulder bags, it doesn't matter, and for backpacks, STM and Brenthaven backpacks are outstanding. Not sure about other companies.
Look at Max_Altitude's reply. Some people swear by Crumpler or STM, but Tom Bihn and Waterfield bags are also supposed to be good. Acme Made sells very fancy, trendy looking bags, and Knomo (which isn't even in the Mac Guides.....*hint hint*) simply makes super expensive, luxury laptop bags.