Javascript is not a compiled language and Node.js is Javascript. It will be executed and interpreted at runtime. You can process your javascript with tool like grunt.js for example lint-test and uglify it, but be careful so that do not break the npm system since it is based on certain conventions.
To package your javascript for distribution in the node.js context build an npm module. https://www.npmjs.org/doc/developers.html
For distributing javascript to the desktop client: Remember it's Javascript an it need to be executed in the Javascript VM. So to have some UI you need to run it in the browser or you need to have some webkit compiled dll to run your code... something like this... http://www.tidesdk.org/
You can also use: http://github.com/rogerwang/node-webkit (Thanks to @edi9999)