Reusing Colors discusses how to reuse "the same colors multiple times within a project even when you are using different programs." This involves several tips, including some downloadable scripts and expressions for After Effects.
For more on color see Color memes and schemes and other posts tagged as color. Other related recent tutorials include Maschwitz on a Blockbuster Film Look and Maltaannon’s Kuler Workflow for AE.
Update: Jeff Almasol noted that the Swatch You Want script was updated to display larger swatches if there are 8 or fewer colors in the file. It's part of Additional Scripts for After Effects CS4 at Adobe, which "contains scripts for editing keyboard shortcuts (KeyEd Up), launching scripts (Launch Pad), create project folder hierarchies (Folder Setup), converting Adobe Swatch Exchange (.ase) files (Swatch You Want, kuler Shapes)... [etc.]"