Geany provides support for detecting and converting character sets. So you can open and save files in different character sets and even can convert a file from a character set to another one. To do this, Geany uses the character conversion capabilities of the GLib.
Furthermore, Geany detects an Unicode Byte Order Mark (see http://en.wikipedia.org/wiki/Byte_Order_Mark for details). Of course, this feature is only available if the opened file is in an unicode encoding. The Byte Order Mark helps to detect the encoding of a file, e.g. whether it is UTF-16LE or UTF-16BE and so on. On Unix-like systems using a Byte Order Mark could cause some problems, e.g. the gcc stops with stray errors, PHP does not parse a script containing a BOM and script files starting with a she-bang maybe cannot be started. In the status bar you can easily see whether the file starts with a BOM or not. If you want to set a BOM for a file or if you want to remove it from a file, just use the document menu and toggle the checkbox.
If you are unsure what a BOM is or if you do not understand where to use it, then it is not important for you and you can safely ignore it.