Hi mmatthes,
You can indeed include Javascript in pages, either through a custom component added to specific pages, or via the wrapper of a skin for inclusion across the community. You can either add your own script tags, or you can use the "liaAddScript" directive in FreeMarker, which will insert your JavaScript near the bottom of the page.
Here's an example of using JavaScript in a custom component:
http://lithosphere.lithium.com/t5/Developers/Ajax-search-Before-Post-Freemarker/m-p/23874/highlight/true#M117
I hope this helps!
-Adam
