I find when working on a project, all the little things add up - especially when it comes to saving time and being organized to make production easier. Approaching the colored labels in After Effects, they can be extremely helpful especially when dealing with larger files containing a vast amount of assets - and particularly when those assets are very similar in nature but you need a way to digest or create further structure.
In the project called out here, I had an animation composed of dozens of smaller animations that I needed to control within the composition. By breaking them down into rows, which was my preference at the time, and assigning colors to them respectively - you can see it will make your brain a lot happier when it comes to digesting everything on the screen, and allow you to spend a little less time fumbling around on the way to your goals.
This is one example, but it's a great application for pretty much every situation. Even on smaller projects I still usually always have a system going where I define a different color for my different content and elements - whatever keeps that particular workflow easier to negotiate.