Is there a reasoning to how often and long the notification light blinks?
Some apps will use the LED to indicate that there is a notification. For instance, the LED blinks green for me when I've received an e-mail message and blinks blue when Twitter has a message for me.

There's no consistency as to how to manage these, however. For instance Google Voice has it under Menu | More | Settings | Sync and notifications | Light, but no way to choose the color. Gmail doesn't offer any way to control it.