Small Web Projects
If it is on the smaller side I typically go with something like this:
Node Modules Unless you are writing everything from scratch (which you probably shouldn't) then this is sort of required.
Config Holds any config or json files that I might need for the project. Typically used for setting up the server.
Libs is for any libraries I make. An example would be a function that fetches data from a third party API.
Routes On larger websites with 10+ pages I typically use a routes folder. Common when using expressjs or other similar frameworks.
Public is the same as your standard website folder. It holds all your HTML files, CSS, imgs, videos, and so on that is open to the public.
package.json This is used to track what packages you are using. Even if you don't have any it contains other information and most servers require it.
procfile is a file used for heroku, but a few other server providers use it as well. It tells them which file the server is supposed to run. It looks like this:
web: node app.js