In node.js, it seems I run into the same 3 filenames to describe the main entry point to an app:
express-generator
package, an
Where I work, we didn't really settle on a format, so we have some apps with index.js, some with server.js. Also, in some we have a config.js file at the root level, others are in a config folder (so require(config/config.js). We even have one where server.js is in a server folder.
The trouble comes when we want to automate our deployment process. It becomes like technical debt when we have to make a bunch of minor modifications for each service.
That said, pick a format that makes sense to you and stick with it.