Wow...this post made me think I shouldn't even attempt to run my own server infrastructure for my startup. This kind of analysis is way deeper than I'm currently capable of.
Hell, we're now infrastructure-less. No VM's (except for our QA to test on, doesn't count), no static servers we can't just destroy and spin up another of in <5 mins, and no database servers that we have to manage.
We used Azure SQL for our RDBMS requirements, and blob/table storage for our NoSQL stuff. Sure there's a server behind it, but it's transparent to us and it's geo-redundant and replicated. When i say "no servers" what I mean is, we don't need any system admins and very little ops folks. In fact at the moment, devs are pretty much ops since we need very little of it.
I also forgot to mention we have a build server, but thats just a virtual machine that we backup regularly. It's our only piece of static infrastructure. Everything else, except storage which is, again, transparent to us, is destroyed on a weekly, if not daily, basis for new releases.
Logging to files creates a lot of headache. I would say the tail plugin for Fluentd (the open source log collector that I am a maintainer of: www.fluentd.org), I would say 1/3 to 1/2 of the questions are related to tailing log files.
I think, fundamentally, files are the wrong abstraction for log data (as pointed out by Adam Wiggins of Heroku fame: http://12factor.net/logs), but it is something that we are stuck with.
Unless you're really unlucky/using young tech/bad at programming you won't need that kind of expertise unless you have the kind of traffic which means you can afford to hire that expertise.
It truly is a joy.