The Ballenburg outdoor museum has umbrellas you can rent, which could make it a rainy day activity depending on how adventurous you are. St. Beatus Holen (Caves) on would make a great rainy-day activity, too. We took a trip to Bern on a rainy day. We usually rent a car so on another rainy day we did a cross-country drive to Gruyeres with some beautiful scenery.
Also, don't knock the mountain top excursions off your list just because it is raining on the valley floor. On our last trip we had really wanted to take the Brienzer-Rothorn Bahn (steam train) trip to the top of the mountain. It was raining but we took a chance and were blown away by the warm sunny weather above the clouds. It was stunning to see all the mountain peaks rising up out of the clouds below. It was a very different, but equally as beautiful view than if it had been a clear day in the valley.