I really don't think ImageMagick is the right tool for this job. It'll rasterize the PDF, for one. There are custom tools for whitespace cropping like SoPDF and BRISS that are both more user-friendly, and keep the PDF in a text-format (if it started that way anyway).
If you do start out with a scan, I'd still recommend BRISS, since it provides a very nice GUI for selecting the crop region, which I think is probably more effective than using ImageMagick's fuzz detection to determine the crop region.
I describe them, and a bunch of other methods I've found effective in this blog post:
Reading PDFs on portables
It relies heavily on things I've learned as a MobileRead member.