One of the main differences I noticed was that PHP-Nuke is no longer an integration of the standalone version

The main changes are:

- Added Freelancer support
- Added Aliens VS. Predator 2 support
- Added GTR2 support
- Added: player sorting to zones
- Added: extra UT3 mutator information
- Added: option to show list totals
- Added: warnings when host has function restrictions
- Added: SQL table creation for old MySQL 4.0
- Added check for .GIF map images ( when .JPG is not found )
- Added config option for hiding offline servers
- Added text to config for easier customization.
- Fixed compatibility with MySQL strict mode.
- Fixed admin login problem on stand-alone version.
- Fixed: UT2004 problems
- Fixed: Quake World problems
- Fixed: Quake 2 problems
- Fixed: incorrect image paths for some hosts
- Fixed: problem when php-nuke uses more than one db
- Fixed: feed not handling offline servers properly

You can download the standalone version heree

And the PHP-Nuke version here

Be sure to check out his site http://www.greycube.com