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 prepended to it: 
PHP removes all whitespace, so a random  in the middle of the code messes up the entire thing. As I mentioned, I can't actually see these characters when I open the file in gedit, so I can't remove them very easily.
I googled the problem, and there is clearly something wrong with the file encoding, which makes sense being as I've been shifting the files around to different Linux/Windows servers via ftp and rsync, with a range of text editors. I don't really know much about character encoding though, so help would be appreciated.
If it helps, the file is being saved in UTF-8 format, and gedit won't let me save it in ISO-8859-15 format (the document contains one or more characters that cannot be encoded using the specified character encoding). I tried saving it with Windows and Linux line endings, but neither helped.
If you need to be able to remove the BOM from UTF-8 encoded files, you first need to get hold of an editor that is aware of them.
I personally use E Text Editor.
In the bottom right, there are options for character encoding, including the BOM tag. Load your file, deselect Byte Order Marker if it is selected, resave, and it should be done.
Alt text http://oth4.com/encoding.png
E is not free, but there is a free trial, and it is an excellent editor (limited TextMate compatibility).
In PHPStorm, for multiple files and BOM not necessarily at the beginning of the file, you can search
\x{FEFF}
(Regular Expression) and replace with nothing.Same problem, different solution.
One line in the PHP file was printing out XML headers (which use the same begin/end tags as PHP). Looks like the code within these tags set the encoding, and was executed within PHP which resulted in the strange characters. Either way here's the solution:
Use Total Commander to search for all BOMed files:
Elegant way to search for UTF-8 files with BOM?
Open these files in some proper editor (that recognizes BOM) like Eclipse.
Change the file's encoding to ISO (right click, properties).
Cut  from the beginning of the file, save
Change the file's encoding back to UTF-8
...and do not even think about using n...d again!