Yes you can use any programming as the template file is compiled with all the classes code before it is sent to the browser, so you can use JS or CSS normal in any template or class.
I have treid inputting the java into the welcome area class and it shows up on the home page but the function of the item wont work.
Basically i am trying to input a "Liveclock" function as i think this would be a lot nicer than the static clock we have at present. The script is all written and i had it running on other sites, but can seem to get it running on this one. I'm sure that other users would like this feature.
Basically what it does is looks at the users local time and displays the clock in a format chosen by the webmaster and updates every second so that it looks like a live clock.
Would admin consider adding this as a future enhancement??