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In the Unix/Linux world, many programs attempt to spruce up quotes by using both forward single-quotes (') and backward single-quotes (`). For instance: `a quote' looks nicer than 'a quote', and ``another quote'' looks nicer than "another quote". However this often does not look right with TrueType fonts. Typically the single-quote/apostrophe glyph is vertical (|) instead of slanted (/), so you get a mismatched pair (\...| or \\...||) instead of a matching pair (\.../ or \\...//).
In the Windows world, a similar trick is used by many word-processing applications, often called ``Smart Quotes''. However instead of the regular quotes, special matching characters are used. Since these characters are not in the standard ISO-8859 character sets typically used under Unix, these glyphs are ignored by Linux font servers and the like and are often not even available for use with documents that were created under Windows, leaving unpleasant boxes in the place of quotes.
It is probably possible to modify the various TrueType font renderers to use a hacked character set that replaces the standard quotes with matching ones. If anyone has done so, please e-mail me, I'd like my quotes to match up and I'm sure many others do as well!