I have a CSS file that looks fine when I open it using gedit, but when it\'s read by PHP (to merge all the CSS files into one), this CSS has the following characters prepend
I don't know PHP, so I don't know if this is possible, but the best solution would be to read the file as UTF-8 rather than some other encoding. The BOM is actually a ZERO WIDTH NO BREAK SPACE. This is whitespace, so if the file were being read in the correct encoding (UTF-8), then the BOM would be interpreted as whitespace and it would be ignored in the resulting CSS file.
Also, another advantage of reading the file in the correct encoding is that you don't have to worry about characters being misinterpreted. Your editor is telling you that the code page you want to save it in won't do all the characters that you need. If PHP is then reading the file in the incorrect encoding, then it is very likely that other characters besides the BOM are being silently misinterpreted. Use UTF-8 everywhere, and these problems disappear.