1) The best converter I've found is Abbyy FineReader (for both OCR and text-based PDFs).
Unfortunately PDF conversion often leaves a lot of unwanted carriage returns / newlines and incomplete lines dangling. Does anyone know of a program to fix this? It's a drag doing it manually via regex in an editor. Calibre sort of does it, with mixed results (maybe I just haven't mastered it.)
2) Another option is to reformat the PDF for a 6" screen using k2pdfopt:
http://www.willus.com/k2pdfopt/
It's a pretty amazing program.
3) Honorable mention goes to Koreader, though I find it doesn't work with all PDFs.