We will soon release a new version of SETI@home, based on BOINC, a general-purpose platform for distributed computing projects like SETI@home. Eventually other distributed computing projects (like Folding@home and ClimatePrediction.net) will also use BOINC, and you'll be able to share your computer time among projects of your choosing.
No exact time table yet, but it looks like you will need to replace your Seti@Home client sometime in the next month. The new client looks pretty nifty, it's supposed to be a general platform for distributed computing. You will be able to pick and choose from a list of which projects you want to do work for and let it take care of everything else.
Jay