Have Swiss-Germany Flexipass. What portions are excluded?

The coverage of your pass is defined in the map and brochure sent with it, and that brochure refers you to the Eurail app, as well. On the rail map, see the blown-up version of Switzerland. On your counted rail travel days, you have full coverage on all the solid rail lines and the lake boats. Some of the lake boat info either changed or was miscommunicated earlier this year, but the latest info is that the boats are fully covered. A version of the bonus list is also at http://ricksteves.raileurope.com/rail-tickets-passes/eurail-germany-switzerland-pass/index.html, on the tab for Travel Bonuses. Each item is either covered or discounted, not both. Discounts don't require use of a counted travel day.

Dotted train lines, as shown for Interlaken-Muerren and the rest of that valley, offer a 25% ticket discount any time that you just have the pass in hand. The discount applies on the Schilthorn lift as well as the Jungfraujoch train. For this region, see also http://www.jungfrau.ch/en/tourism/travel-information/tickets-rates/interlaken-ost/fares-for-individual-travellers/, click the link for "Discounts" and the click "Eurail" to see all the discounted lines in yellow. Always show the pass to request a discount if buying a ticket, since the various published lists may not be not complete, and/or not completely in agreement.

I had a Swiss/French pass, the day I knew we wanted to do the Schilthorn I went into the ticket office at the train station that morning and told the agent that was my plan. He looked at my pass to confirm and then sold me a discounted ticket for the Interlaken onward portion of the trip, which consists of a small clicky-clack train to Lauterbrunnen, a bus through the valley, and then several cable cars to the top. You can also take a cable car from Lauterbrunnen and then a small train to Murren. Other posts describe this better than me. IIRC, each ticket that day was about 100 CHF.