Well, I searched the net and managed to find a way to overwrite the web-browser's "alert" box.
I am unsure how it will work on linux and mac's. Can anyone here want to see?
http://www.geocities.com/sagefankia/index.html
The button on the page pops up the alert window.
The style is loaded with css and the popup is initiated and handled with java functions. View the source to see what it is like.
The original code page is here, along with their example:
http://slayeroffice.com/code/custom_alert/
The fifth or so paragraph down states how it stops user interaction while the window is open.