Suhosin is an advanced protection system for PHP installations.
fuzzy notepad - PHP: a fractal of bad design
Coding Horror - The PHP Singularity
ircmaxell's blog - PHP Sucks! But I Like It!
Upload-Point is a very simple to use php upload script with password protection.
w2box is a simple php script which allow you to upload and download files. There isn't any complex user management because it aims more for private file repository use. Creative Commons license (non-commercial use).
ByteHoard is a web-based application for remote file storage. Needs MySQL
dodoupload
PHCDownload A file content mangement and manipulation system. Needs MySQL. A lot (too many?) options on the file upload form.
Silentum Uploader allows visitors to upload files to your site quickly and efficiently, without the use of MySQL. It uses only two PHP files, and can be set up in a matter of minutes.
snif - simple and nice index file Server generated directory indices are ugly. OK, they work everywhere, but they're still ugly. If you'd like your download directory to be maintainable without creating and changing huge HTML files, just put snif as its index file into the directory and here you go!
phpFileManager
phpXplorer
XQTO File Manager
osFileManager