I use an M-51 Engineering Bag that I picked up off of Amazon. It's small enough to not be awkward and obtrusive, but has plenty of pockets and storage for a lot of different stuff.
Here it is with the iPad on top front to give you an idea of size.
With the front flap open, you can see a lot of the little pockets that are available for pens, notepads, and other stuff. The flap has a clear plastic pocket for maps and other stuff you may need quick access to.
A quick look inside the main pocket. Plenty of room for the iPad and some notebooks. There's piece of plastic lining the back and separating the front main pocket from the rear pocket and maintaining shape when the bag isn't full.
The back zips open for access to more storage pockets for miscellaneous stuff.
It's a great bag that I've had for a couple years now and has held up to some abuse. Before the iPad, I used it to carry a netbook, and it did the job just fine. If I had to do it all over again, I'd go with a black or khaki color over the olive drab, but that's a small quibble really.