Aug 16, 2011 - 1:17 PM
Many Swiss railroads are private companies, but you don't need to worry about that. Just take a look at the map linked from the Swiss Half Fare Card page and you'll see what's included. The Jungfraujoch is included as well.
Tickets purchased through the Swiss railways are priced the same everywhere, but other resellers may charge less or more.
I don't know about buses. The train is the most obvious way to travel, especially if you already have a pass.