I've been a long time coming, and I'll be a long time gone. You've got your whole life to do something, and that's not very long.
Ani DiFranco (American singer, songwriter, and guitarist)
The Timeline is After Effects' killer application. It is the reason above all others that After Effects is equally effective for motion graphics or visual effects work. Node-based compositors make it easy to see render order, but they can make coordinating the timing of events more difficult.
In 7.0, the Timeline has only become even better with the addition of the Graph Editor, a new user interface for editing multiple animation curves at once.
The Timeline even makes render order explicit if you know how to view it; 2D layers render beginning with the lowest in the stack and ending with the top. Properties of each layer (visible by twirling down) render in top-to-bottom order. Chapter 4, "Optimizing Your Projects," further explores the render pipeline.
With the Timeline as the center of your compositing process, you can always investigate how elements and timing relate. You could argue that render order is more significant than timing for visual effects work, but once you get the hang of managing the Timeline well, render order is no longer as much of an issue.
The Timeline panel is also a relatively user-friendly part of the application, albeit one packed with hidden powers. By unlocking those powers and mastering them, you can streamline your workflow a great deal, setting the stage for more advanced work.
One major source of hidden powers is the Timeline's set of shortcuts: A lot of what you can accomplish in the Timeline can be accomplished more efficiently and effectively using keyboard shortcuts and context menus. My feeling is that these are not extras to be learned once you're a veteran, but small productivity enhancers that you can learn gradually all the time, enhancers that collectively offer you a good deal of extra momentum and confidence as an After Effects artist.
Section I. Working Foundations
The 7.0 Workflow
Selections: The Key to Compositing
Optimizing Your Projects
Section II. Effects Compositing Essentials
Rotoscoping and Paint
Effective Motion Tracking
Film, HDR, and 32 Bit Compositing
Section III. Creative Explorations
Working with Light
Climate: Air, Water, Smoke, Clouds
Pyrotechnics: Fire, Explosions, Energy Phenomena
Learning to See