Similar to Wendy's structure, we define the company-wide set of projects as Epic User Stories defined on a company "team" (or to confused things, what Rally defines as "Project") which is good for the fiscal year, then we define the "teams" as all the Scrum Teams within some light organizational structure (groupings of teams). This provides you with a team/project matrix which gives you multiple views of your stories. It is relatively easy to add/move teams as your company changes. We are in the 6th year of this structure and have little complaint. The relatively new Portfolio module gives you further structure to plan/manage work as a Portfolio or Product manager where the Epic "Project" Story moves over to the "Initiative" story with User Stories rolling up to Features, Initiatives, and then Portfolios. We are still experimenting on the Portfolio structure and use.