since I made some efforts reading PDFs on my Pocketbook e-reader - thanks to this forum - I wrote down my "Best practices" in my wiki. It is not just about PDF's, but also how to convert the files, contrast enhancement, cropping and all the stuff. There are some handy bash scripts (tested under Ubuntu 11.10) for batch conversion.
This article was written mainly for the needs of e-Ink devices.
If you are interested, feel free to read the article here
. I am more used of the mediawiki syntax, than forum syntax, so it was easier for me to get things done in my own wiki.