I assume this question is mainly related to setting up your online server, not a local computer.
On irc, someone answered the same question and said that he was using a separate user for each application. Therefore, I suppose this is a good common practice.
I mainly do / home / user / apps
I see a lot of nginx examples, so I guess this is what most people use. I have a server with varnish in front of a node.js application that works well and is easy to configure. There are some clean node.js solutions, but for something as important as your reverse proxy, I would go for something that is a bit more tested in battle.
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