How about effectively dealing with ligatures?
I know that people like to harp on and on about how great LaTeX or InDesign are, and when it comes to complex layouts (particularly LaTeX if there are lots of referenced figures and InDesign for text wrapping, etc.), I agree. If you were writing a scientific article, I'd tell you to use LaTeX. If you were creating a magazine, I'd tell you to use InDesign.
But for your typical, text-only, fiction novel, the kind you're most likely to read on a Kindle? I don't think it really makes a difference.
(And even if they weren't, I would appreciate such examples.)
People make a big deal about how using Word will lock you into a certain format when they're storing their data on floppies or, even worse, rasterizing it and keeping just the PS. Seems like the latter is a lot worse than the former.
I guess they could generate PDFs from Word files with Acrobat and shoehorn them into the process, but any publisher that is actually satisfied with doing that is bonkers.