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PDFs are meant to retain deisng/layout, not reflow like a webpage. That way the document is authored to look one way and when viewed or printed anywhere else it will look identical. The nature of it doesn't allow for conversion to a reflowing format.
That said, it depends on the contents of a particular PDF and what your particular issues are. You can use something like ImageMagick + Ghostscript to convert a PDF to a series of images. Zip them up, rename from *.zip to *.cbz and Calibre will convert that to a mobi for you if you want.
I prefer to just leave the PDFs intact (unconverted) but I run them through Briss which lets you crop the entire PDF to remove all the empty margins around the content so the PDF content ends up a little bit bigger and readable on the kindle.
Another option is copy the content into a word processor to clean up the formatting and export to html and then mobi.
It depends on each particular PDF and how much effort you want to clean it up. But all my PDF reference books are just fine cropped, fit full screen on a K3 and are readable without zooming and I don't lose any formatting that way. I've never yet felt the need to convert.
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