For research articles I do this:
1. crop out page numbers: http://briss.sourceforge.net/
2. remove columns and reflow with: http://willus.com/k2pdfopt/
The later one works like magic, it totally made my ebook reader so much useful. (A Tolino Vision, a very fine german device not locked to the Amazon store: http://mytolino.com/)
(edit: fixed links)