For several years now I've used a Targus backpack to haul around my portable office. A good bag, one that you can trust and has space for what you want to carry is absolutely key. For me, as you will see below, this means I want a lot of space, with large cavernous storage areas. I find my use of other bags (see the next section) helps organize these large spaces without the waste of the designers trying to guess what I want to carry and what shape it will be. For instance, even my favorite CityGear Chicago bag comes with a cell-phone pouch, how useless is this? Cells change shape so often I swear we'll have a boomerang shaped one yet. Let me worry about organization, the backpack is about portability and accessibility. Some small amount of small pockets are great for high access items like pens, pencils, etc but I'll organize the rest, thanks.
I love me some Zip-Lock Bags, these little creations are absolutely fantastic for organizing the internals of your backpack. Now, don't go overboard and turn into Monk or something, but these bags are great for organizing. I've had best luck with the Freezer bag variety because the plastic is tougher. Also, here's a hint : Punch small holes with a pencil in the sides of your bag. This will let things pack small easier as air can escape, and we're not looking to hold liquids in these anyway.
There are endless other bags you might be able to use. Go to your favorite online mega-retailer and search on Zipper Pouch or Zipper Bag and you'll find them. I prefer bags which are more than two sides gusseted together so that I can fit larger items into them. At Tech-Ed 2007 I was given a couple of these wonderful bags (pictured right) which originally were printed with a Windows Mobile logo which has mostly peeled off the non-pictured side. These slightly padded bags have been carrying my portable hard disks and video camera ever since, and I'd love to have more of them (4-6 more would do if anyone has a stack of these in their office, email me).