[Javalicious]

"Best" is probably whatever you're familiar with. If your pre-pdf content is in Word, I'd just run with it -- most 'classic' word processors can handle the export to ebook stuff just fine. I've done exports from Apple Pages without issue.

That said -- if you're looking for a layout that reflows based on the screen size (read: more suited for mobile devices), you might want to look at exporting to .epub rather than .pdf.