What is needed is cross project ranking of some kind. For a team with at least 6 active projects and developers working on multiple projects, each person giving different percentages of their time to each project: should there be a way to rank the importance of issues not by the priority, but by what someone have determined would be the best order in which to tackle problems. The ability in Greenhopper to use the planning board for team wide planning inside each project breaks down at the individual level.
The ultimate goal is to have a page where each user can go and look at all their issues and make sorted todo list in GreenHopper, a page on the Agile section that is designed for personal ranking. On the side would be each project and then the list of issues you are assigned in each. Dragging issues could rank in a separate ranking field, something like "personal priority" could be used for private self organization. This would make it easy to decide on what someone should spend time and not effect how things are prioritized inside of each project.
Also a simple auto prioritize can be handled by managing a slider to show percent of time currently devoted to each project. This would just weigh each project issue's importance based on the percent time that project is allotted. Then the developer could go in and reorder things to their liking.