If you open a file created with the Macintosh version of QuarkXPress, the Windows version has no problem translating the em dash from the Mac 209 to its Windows seat of 151. If this is text that will later be incorporated into printed documents, it will at some point have to be purified. There are a number of ways of going about it, but I advocate the Rigorous Systematic Approach to the haphazard one. The latter consisting of simply scrolling through a document and changing any tick marks you spot to proper quotes, converting hyphens to dashes, removing extraneous spaces, inserting ligatures on the fly etc. Removing all double spaces from a text file is always the first task I undertake.
Ellipses are a good example.
Because some people type four periods to create an ellipsis, you should deal with these before searching for any three-period ellipses. That way, if both varieties happen to be present in the document, you can replace the four-period ellipses first, then tackle the threes, but not the threes before the fours. The dot shape is the same, but the spacing between them is different. Any time you're searching for multiple items, always begin by searching for the highest number and work down. You can't, for instance, replace all straight quotes in a document, which are identical opened or closed, with true quotes, which have two distinct styles for opened and closed.