Will it affect all perl scripts ran? All scripts run by IIS, but not the scripts run from the console, is my impression.

I never used the taint mode and wondering would I need to change a lot of work in my scripts. If you've never used taint mode, I think it's a safe bet you would have to change a lot. However, if you have written your programs in a modular manner, so that you process your input in one place, your changes could quite conceivably be fairly simple to apply.

If the site will have many users, then you should already be checking your input (in effect doing what taint forces you to do, and taint will only help you find areas where you forgot to do it. If you aren't checking your inputs on such a public site, you are sorely tempting fate.