If you don't mind pan and scan (big if), I've never noticed an instance where materials in the PDF were not properly presented. In other words, if the PDF looks good on your computer, it'll look good on the Kindle 3...just much, much smaller. Is it possible to have a font embedded in the PDF that the Kindle 3 would simply not display? I guess it's possible...I haven't seen that yet, though, and I've looked at a fair amount of PDF.
I've tried switching to landscape mode, as well as magnifying, but am not a big fan of looking at chunks of the PDF page at a time. The best solution I've come upon so far is to wear a pair of "reader" glasses that magnify the image 1.5x - 2.5x.