Enabling Javascript is easy! Just add "script[language|type|src]" to the Extended Valid Elements box. If you are not using my "flash hack," that should be the only thing in the box. If you want both, it should look like this:
",
plugins : "flash",
extended_valid_elements : "script[language|type|src]
Also, if anyone is wondering, this should work for any plugin bundled with TinyMCE. You can see a list of bundled plugins here:
http://wiki.moxiecode.com/index.php/TinyMCE:Plugins
Just replace the word "flash" in the example above with the name of the plugin to enable. If you want to enable more than one, add it using a comma separated list, like the following:
",
plugins : "flash, bbcode, layer",
extended_valid_elements : "
However, you may need to add buttons to the button bar to get some plugins to work properly. I have not worked out the injection for that code (simply because it's not something I'll be using).