I’m writing a single page single/purpose web app under Files > web. What are the best practices? Do I use REST API? SDK JavaScript? Do I have to specify the Application ID? If so how do I protect the Application ID? Are there any example applications available (besides the shopping cart)?
Using REST or JS-SDK is directly related of your needs, I advise you to use JS-SDK, it already contains all you need, but if you would like to use your custom library for process API calls be free to use REST.