Currently, to create a NodeJS pad, you have to create an HTML pad, open up a shell/console output tab, and enable use custom server in settings. Ideally, there should be a NodeJS project type that has all of this set up with appropriate template code. At that point, we could also remove "use custom server" option from HTML pads as it is likely confusing for most people who only want to create HTML pages.
Moving this out from our internal issues list.