检测文件是否为UTF-8带BOM格式的方法其实就是取文件的前3个字符进行检测即可，代码如下：

<?php
$auto = 0; //不自动删除文件中的BOM头
function checkBOM ($filename) {
	global $auto;
	$contents = file_get_contents($filename);
	$charset[1] = substr($contents, 0, 1);
	$charset[2] = substr($contents, 1, 1);
	$charset[3] = substr($contents, 2, 1);
	if (ord($charset[1]) == 239 && ord($charset[2]) == 187 && ord($charset[3]) == 191) {
		if ($auto == 1) {
			$rest = substr($contents, 3);
			rewrite ($filename, $rest);
			return ("<font color=red>BOM found, automatically removed.</font>");
		} else {
			return ("<font color=red>BOM found.</font>");
		}
	}
	else return ("BOM Not Found.");
}
function rewrite($filename, $rest) {
	fseek($filename, 0);	//跳转回文件的开头
	file_put_contents($filename, $rest); //将$rest字符串的内容写入文件$filename
}

echo checkBOM("D:withBOM.txt");

然后，添加一个遍历目录的函数即可进行批量检测/删除：

<?php
if (isset($_GET['dir'])){ //设置文件目录
	$basedir = $_GET['dir'];
}else{
	$basedir = '.';
}
$auto = 0;
list_dir($basedir);
function list_dir($basedir){
	if ($dh = opendir($basedir)) {
		while (($file = readdir($dh)) !== false) {
			if ($file != '.' && $file != '..'){
				if (!is_dir($basedir."/".$file)) {
					echo "filename: $basedir/$file ".checkBOM("$basedir/$file")." <br>";
				}else{
					$dirname = $basedir."/".$file;
					list_dir($dirname);
				}
			}
		}
		closedir($dh);
	}
}
function checkBOM ($filename) {
	global $auto;
	$contents = file_get_contents($filename);
	$charset[1] = substr($contents, 0, 1);
	$charset[2] = substr($contents, 1, 1);
	$charset[3] = substr($contents, 2, 1);
	if (ord($charset[1]) == 239 && ord($charset[2]) == 187 && ord($charset[3]) == 191) {
		if ($auto == 1) {
			$rest = substr($contents, 3);
			rewrite ($filename, $rest);
			return ("<font color=red>BOM found, automatically removed.</font>");
		} else {
			return ("<font color=red>BOM found.</font>");
		}
	}
	else return ("BOM Not Found.");
}
function rewrite($filename, $data) {
	$filenum = fopen($filename, "w");
	flock($filenum, LOCK_EX);
	fwrite($filenum, $data);
	fclose($filenum);
}
?>

代码收集，方便自己随时查看。