Helper files are a pain in the ass because they're usually all jumbled up and hard to maintain. In my experience with them, they come a zillion functions that are all unrelated, from input sanitization to XML processing to database initialization. Then, when you need to figure out what the hell is going on in your code, you have to wade through a forest of garbage just to figure out what the function is doing. God forbid you accidentally make a typo in ANOTHER function while editing the one you wanted -- now you've just introduced another bug without even realizing it.

Furthermore, in PHP, we devs are almost always using the same boilerplate over and over again (getting user input, etc.), so why would we use a "helpers.php" file when we instead could break out our code into more semantic, reusable chunks?

Instead, you should be creating classes (or at the very least, creating files that all have related functions, not just throwing all of your "helpers" into one file, so instead of helpers.php, you have inputSanitizer.php, htmlParser.php, et cetera).

For example, I see a lot of this kind of thing in "helper.php" files:

    function sanitizeInput($input) {
        $input = htmlentities($input);
        ...
        return $input
    }

What I personally love to do because I'm OO obsessed is use a home-grown InputSanitizer class, so now when I have a new project, I don't have to copy over my "helpers.php" file and then strip out everything unrelated to my project; I just copy over InputSanitizer.php to the new project and do something like this:

    $username = InputSanitizer::getPostData('username');

MUCH cleaner and easier to maintain. Even better: if you're using classes and auto-loading, you'll never have to worry about includes again, you simply just call the class methods or instantiate.

There's a clean, wonderful side to PHP that I think a lot of people aren't taking advantage of.