I think making your own panniers is a great idea. I have a sewing machine designed for sail making that is just perfect for this. I think one of the best point in the PDF above, though, is where he says that making your own paniers is worth it if you
have your own ideas. It's pretty tough to save actual money over something like the paniers offered by say MEC, well proven, cheap, not waterproof unless you use a rain cover, or line them internally, but the same likely applies to any home made one also. I think it gets interesting when you thing really custom. If your thoughts take you to a place retail doesn't visit then home building them is your only choice.
For instance I make my own racks also, so I can configure the rack and bag to eliminate hooks, it light it's strong, and no hook rattle.
Here is another design I quite like. provides the oppportunity to use dry bags to keep the stuff you want dry, and to provide stuff bag based organization. Probably not the best choice for a trip through a lot of urban landscapes.
http://www.backpacking.net/makegear/panniers/index.html