Matt Gemmell on what he calls the "Critical Customisation Cost of Software":
Geeks are known to love configuring and customising their devices, but perhaps paradoxically they can also be reluctant to do so because of a compulsion to not deviate too far from a “clean†(and thus presumably safe, fast, efficient, known and well-tested) configuration.[1]
I'm part Felix, part Oscar. When I get a new machine and start customizing it, I'm just obsessive enough to document what I'm doing, so that my deviation from "clean" will be reproducible. But I'm not obsessive enough to maintain that document over time as I install more apps and tweak more settings. As a result I feel a constant nagging distress over how messy I've let my computer get — how far from pristine. I'm sloppy in other ways too, that I keep meaning to clean up One Of These Days.
I know this is irrational, but one thing that bugs me is apps that insist on being installed in /Applications. I don't like third-party apps getting mixed in with built-in ones. The Mac App Store has forced me to endure a bit of this discomfort. I used to put my third-party apps in special subdirectories of /Applications, named with leading underscores so they show up at the top in Finder. Now I put them in ~/Applications — the ones not from the Mac App Store, that is.
[1] One sign of my OCD[2] is that I checked the HTML source of Matt's blog post to see if he'd italicized the commas in "safe, fast, efficient, known", because I wanted to be sure to quote him exactly, down to the punctuation. I was glad to see he italicized only the words, not the commas.
[2] Like Matt, I don't claim to suffer from clinical OCD. I'm just using the term as a shorthand for the fussy side of me.
Andy – you can certainly move apps from the App Store from /Applications to ~/Applications.
Also, be aware that some apps don't like this (1Password comes to mind – check your logs if you move it out of /Applications).
As far as using a clean machine, I just have a script that I run on any new machine I install. It sets my prefs and installs some basic things that I want everywhere (like MacVim).
Thanks, Ed — good to know re: ~/Applications. As I recall you keep your script in either git or Dropbox (though I saw your tweet about Dropbox, so I bet not there), which is also a good idea.
I keep that script both in a git repo stored on a cloud-service drive. There have been a few alternatives to DB that seem to understand security a bit more. I'm still using Dropbox for some very ephemeral shared data – but absolutely nothing executable, like a script or binary.