Don't get soft-sided ones, as you will then have to buy the brakets that keep them from flopping into the rear wheel, and they flop around and look like crap when they are empty- get rigid ones.
I bought a pair of Willie and Max bags that toss over the rear seat. I cut a small notch in the connector piece to clear the ignition box, and they now fit under the rear seat. I don't use them much though, as I just don't like the looks of saddle bags, and they are not quite big enough for my laptop computer I need for work and grad school. I bought a rigid sissy bar bag that slips over the seat back, and use that a lot more. It will hold enough stuff for my grad school classes or a couple days out of town, plus my computer, and it came with a slick little waterproof cover.