I've been scanning books and magazines also - mainly for reference (and using a PRS-700), and it beats having a trunk load of books in your car. To cut them I use a Black and Decker workmate (also used for other DIY projects around the house), a Dremel, 4 clamps, and two aluminum L-shaped channels.
The setup is simple, I lay the magazine open on the Workmate with the cover facing up. I use the L-shaped channels and the clamps(see hardware store) to hold down the magazines, and use the Dremel for cutting.
The Dremel with a thin cutting wheel slices through magazines like butter. Before the Dremel I used two different cutting boards - one with an arm, and the other used a sliding cutter. With the boards, I was limited to 3-4 sheets at once. It also took time - about 30 minutes for a 250 page magazine. The Dremel brought that time down to about 3 - 5 minutes. In about a 1 hr I am able to do a years worth of magazines.
For glued bindings on hardcovers it takes a bit longer. The glue tends to melt and gunk up the cutting wheel too, but it's safer than using a knife. Also I found that I still needed to use a cutting board afterwards to clean up the jagged edges.
There are only two drawbacks to my method:
1. Dust - The cutting wheel generates a lot of dust from the cutting of the media.
2. Heat - At faster speeds any binding of the wheel (if held at an angle) will burn the media.
To counter the dust, I have to vacuum each single page clean. Otherwise, the dust builds up in my Fujitsu Scansnap and it results in funky little streaks when doing color scans.
My pet project is to somehow add hinges to the L-channels, so that it is more like a cover that holds down the media. The channels would have to be mounted either onto the Workmate or some other framework - the idea being that I can easily remove them so I can use the Workmate for other things.
Here are the type of clamps I use to hold the L-Channels down:
Irwin One-Handed 6 in Mini Bar Clamp 4 Pack - Model 5464
L-channel sample:
http://tiny.cc/vpAWq
(Wear safety goggles with the Dremel!!!! If the cutting wheel binds, it can break into shrapnel)