you need to determine how you will deliver your program to end users. If you are going to have users initiate your program via a website & browser, you'll need jave or ms activex. Otherwise the target workstation would probably need something installed on it, and that can be a problem.
Also is your audience all on one platform, or do you have some users with MS, some Macs, some linux? The answer will also have a lot to do with your final decision of a coding environment
You can use PHP to write batch scripts in both windows and linux, as long as php.cli is installed. No web server or web application necessary. I once wrote a php script for linux that read track titles from an audio CD, and then generated a CDDB file for the CD (mostly for home-recorded cd's that didn't exist in CDDB databases). The script was entirely done with PHP and runs from the command line.