There's actually an option in Xcode to do this. In v. 3.2.3:
Project menu -> Edit Project Settings -> General tab -> Organization Name
(Found it by chance when following someone else's tip on importing a project done with an old SDK.)
In Xcode 4 (Developer Preview 5), in the navigation pane (far left side), select the project (top item).
Expand the Utilities pane (at window top-right, far right button in the 3-button "View" group).
In the "Project Document" section is the "Organization" text field (File Inspection view, second section from top).