There are two kinds of people in the world: people who like a nice, clean virtual workspace, and John Siracusa. If you're closer to the former than the latter, check out Hocus Focus - a Mac menu bar app which automatically hides inactive apps.
At first, Hocus Focus may remind you of Spirited Away (no, not the Japanese animated fantasy film) another Mac app which did something similar. However, according to MacUpdate, Spirited Away hasn't been updated since November 2009. Hocus Focus also has some additional features which make it much better.
When you first start it, Hocus Focus will default to hiding inactive apps after 30 seconds. That's a good, basic starting point. However, there's no need to stop there. You can change the hiding time on a per-app basis, or disable hiding for certain apps (drag the time-slider for an app all the way to the left, and it will join a "Disabled" group at the bottom of the list), or you can have apps hide immediately after they lose focus. For example, as soon as I am done with Activity Monitor, I want it hide itself immediately so I don't see it updating in the background, which can be distracting. On the other hand, I often want to keep Tweetbot visible in the background, so I might not want that to hide at all. If I am in the midst of sending messages to someone, I might want to give Messages.app a little extra time before it hides itself, but if I haven't used it in, say, five minutes, then it can hide itself.
Last but not least, you can create different Profiles in Hocus Pocus. Each profile can have a different default hiding time (for example, 60 seconds instead of 30), and you can have different settings for which apps to hide, or not hide, or how long to let them be idle before hiding. I created a profile where everything hides after 15 seconds except for MultiMarkdown Composer and Marked 2, which I used while writing this article. My only complaint is that Hocus Focus' profile switching feature using ⌘+\ as its hotkey, which has been 1Password's keyboard shortcut for time immemorial, but you can easily change it in preferences.
Hocus Focus was on the Mac App Store under the name Houdini. The app is no longer in the App Store due to concerns about "App Store rejections and rule violations" (understandable, especially if you're familiar with Apple's move towards sandboxing). The move away from the App Store also means that updates will be available to users more quickly.
Hocus Focus is free, but donations are accepted.