Here's a tip that won't be news to any hardcore After Effects CS4 users, but lately I've encountered artists working in CS4 who don't know about it, and to me it's like not knowing that you can switch apps on a Mac with command + tab, just like alt + tab on Windows. It's possible someone out there even just received a bonus tip.
Anyhow, CS4 had some major additions - the OEM of MochaAE pretty much pays for itself - but the feature I miss the most when I find myself back in an earlier version of the software is Miniflow, which adds a microscopic tree-node interface to the world's least nodal compositor. Navigating nested/parent comps is visual, intuitive and literally available at the touch of a button.
Okay, suppose you knew that. Did you realize you can hit S with the UI open to resort the stack alphabetically? And of course if it seems wrong that the default flow goes in the Hebraic right to left direction, as has been asserted elsewhere, you can change that too.
Me, I leave it as-is. The old way of having the master comp naturally at the left and subcomps open to the right is still the way it is in the Comp panel.