Obviously this is too late for you but others may benefit.......
Between Geneva and Zurich I'd stay in Spiez. This is a great location for anyone on a railpass and, for reasons which I've never worked out, accomodation is much cheaper than nearby Interlaken. Possible rail excurisons from here:
Bern - especially as a wet day standby because the old streets are arcaded.
Luzern - out via Brunig Pass line and back via Emmental - note some railpasses are valid on lake boats in Luzern.
Montreux via Gstaad (this is the direct route from Geneva anyway).
also train to Meiringen (yes, the one out of Sherlock Holmes) then Postbus over the Grimsel pass to Oberwald and train back via Brig. But note that most railpasses are not valid on the bus and some are not valid between Oberwald and Brig so you'll have to pay for that bit. Also. make sure train from Brig to Spiez calls at Kandersteg, those that don't may go through the new tunnel and there's nothing to see there!
In the Black Forest, Villingen is a nice, well placed town and easy to reach from Zurich (change at Singen). Special note for people with railpasses that allow a number of days over a longer valdity. When you pay your local resort tax at accomodation at most places in the Black Forest your guest card should have a "Konus" logo on it. This entitles you to free use of buses and regional trains over a huge area - so you can save the days on your pass for somewhere else! The local tourist should have a leaflet with a map of the Konus area (which will be even bigger in 2008).
For me, the final place before Munich would be Mittenwald. High in the mountains on the border with Austria and a short ride to Innsbruck. From the Black Forest travel via Lindau (on the German shore of Lake Constance) - Kempten - Garmisch Partenkirchen.