I always fold mine being careful not to have a crease over a bar code. Fortunately, the current positioning of bar codes make it possible easily to fold the A4 sheet several times. This was not always the case.
With inkjet printers it's obviously a good idea to keep the boarding passes dry!
The only problem I've had was when the pass was accidentally scanned twice by the security person; Ryanair issued a replacement instantly (this was before 100% OCLI, so there was no fee).