JavaScript Configuration
Roots does a lot of the heavy lifting in JavaScript for you, pretty much out of the box. Also, it comes with several libraries built in, notably prototype, jQuery, mootools, and scriptaculous. Add any other favorite libraries into the /_assets/js/libraries/ folder. In addition to full libraries, Roots has utility functions such as Ajax, an Eolas fix, Robert Nyman's Encapsulated Load Object and DOMAssistant, et al. All this should give you a nice leap ahead rather than writing everything from scratch.
You can load scripts the normal way, using the script tag, or you can link to the /_assets/js/ScriptLoader.js file, and call the ScriptLoader.load(url) function within to add additional scripts at runtime. The ScriptLoader method hasn't been completely tested with libraries, so you may have to load them the first way.
Base.js includes much of the functionality you'll ever need, and is a mix of stripped-out event functionality from prototype, and many utility functions that Robert Nyman or I have written.