If you install a lot of third-party apps, you may have noticed a trend: More and more programs these days run as icons in the menu bar--either solely in that mode or as an option in lieu of (or in addition to) a normal Dock icon. The list of such programs is huge, and includes such prominent apps as Dropbox, ScreenFlow, TextExpander, and hundreds of others. (Disclosure: The company I work for, Many Tricks, produces several apps--including Desktop Curtain, Moom, and Time Sink--that also offer the ability to run in the menu bar or the Dock.)
Putting on my user hat (as opposed to my Mac developer hat), I generally like this trend, especially when it means I have some choice about where a given program appears. Having that choice gives me more control over three key features in OS X: the Dock, the menu bar, and the Command-Tab program switcher.
The Dock: I prefer a lean Dock, one that primarily shows active applications. I keep only a handful of icons there permanently, as I rarely use the Dock as a launcher. I also keep my Dock hidden (more pixels for windows), and occasionally I move my Dock to a different screen edge, depending on what I'm doing. (I usually use the Command-Option-D shortcut to toggle its visibility.) This means the Dock isn't a good place to put icons that convey status information, because first I have to find it before I can see what's in it. For certain classes of programs, keeping them in the menu bar and off the Dock makes more sense.
The menu bar: Unlike my Dock, the menu bar is always visible, and always in the same location. This makes it a perfect spot to keep apps that display information or that I want quick access to but don't need to interact with regularly. What types of programs have I just described? Utility programs, primarily--apps that I have running all the time, but that don't necessarily require ongoing interaction or an ever-present window. The menu bar is ideal for such programs, because I can tell that they're running and I can get to their interfaces, and they're not stuck in my Dock.
The Command-Tab program switcher: This may be the best reason to keep certain programs in your menu bar and not in your Dock--you won't see menu-bar-only programs in the Command-Tab program switcher. It may seem like a small thing, but given that I switch programs hundreds of times a day, this arrangement is a big timesaver: It's much easier to find the program I want when I don't need to navigate through a series of utilities that I rarely access directly.
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