ALT link: http://www.provideocoalition.com/chromatic-aberration-fix
While Creative COW's Carl Larsen explains and shows you how to remove chromatic aberration using After Effects, Lloyd Alvarez at AETUTS helps you keep 'em separated with Shift Channels in Learn how to Create Chromatic Aberration.
A few days earlier Maltaannon blogged about his work on a CustomEffect wrapper for a Pixel Bender experiment he did that would help in Separating RGB channels -- and Forging Fire posted an AEP (After Effects CS3 Split RGB Channels) so you wouldn't have to wait. It uses the Shift Channels filter of course.
Also, it seems like Video Copilot Twitch might make quick work of a task like this. And literature on filters like Tinderbox 2 Lens, Magic Bullet Looks, and Panopticon Lens all say they work with this effect (none were tested here).
Update: Satya Meka has a new free AE filter for this; see New Pixel Bender plug-in: Separate RGB.