Indicator Lights
Don’t care about running or closed

Since OS X Lion I changed the way I use my computer. It's more like iOS where I don't care about if applications are running or closed. I don't even care about if a document is saved or not. It's time to care about the content because the content is the reason why you use the computer.
Indicator lights for open applications
Everything starts here: The Dock is always shown by default and plays a big role in Mac OS X. Since Lion you can turn of the indicator lights for open applications. Apples target is a iOS like experience. For me this doesn't work on a desktop OS.
Lets take a look at iOS: Mail, Messages and the Phone app are always running and you don't have to start them. All applications from the App Store can send you push notifications. Even if they are closed.
Back at Mac OS: No applications are running. No applications can send you messages. You won't receive any Mail, Twitter DM etc. if the application is closed. If you disable the indicator lights for open applications you will properly miss important stuff. And the worst about it: You don't notice it. That's the reason why this feature brings you a big disadvantage.
Fix the problem

Because I'm a SSD user, mostly all of my apps are opening in under a second. To bring the iOS feeling back to my Mac I let all important programs open automatically when I log in. I disabled the indicator lights and also the option “Animate opening applications”. Because I won't be blown away when I start my system I enabled the option “Hide”. Now all programs are running and no one will recognize it. Like on iOS.