I'd skip the Glacier Express. It takes too much time, plus I prefer being outside, on the mountains, and have the time to enjoy the view.
1 day: Instead of Jungfrau I'd do Schilthorn. Way cheaper, less people, and in some sense better view because you see the Jungfrau as well.
2 day: Then the glacier you can check by visiting the Aletsch as suggested below plus Zermatt area
1 day: You could combine Titlis and Luzern. On Titlis try the scooter and devil bikes.
1 day Ticino: Bellinzona, Locarno, up to Cardada
1 day: You could combine Zürich with a great hike to the Grosser Mythen. Or, I you'd prefer a lazy day, then Zürich, Rhine Falls, Schaffhausen, Rapperswil, then take the ship all the way back to Zürich, and finally up to Uetliberg.
1 day Klettersteing in Braunwald, there are routes with different difficulties, and you can rent everything in the hut up there.
1 day: Lausanne, Montreux, Les Diablerets, Glacier 3000
..and don't forget to check SBB's offers of the month: http://www.sbb.ch/freizeit-ferien/ta...-freizeit.html