How do I get from Fussen to Berchtesgaden?

Each of your trips are fairly straightforward, but in some cases will take the better part of a day. Regarding each of the routes you mentioned.....

• Lauterbrunnen to Füssen: You'll first take the local Berner Oberland train from Lauterbrunnen to Interlaken Ost, where you'll connect with whichever train you choose for the next part of the journey. The bahn.de website shows a number of trains you could take, of varying times and number of changes.
• Füssen to Berchtesgaden: Again, the website shows a number of possibilities, most involving a Bus for part of the trip. You'll have to decide which one best fits your circumstances.

Could you elaborate on your reason for the visit to Füssen? Are you going there just to see the Castles? If that's the case, you might also consider staying in Munich and just making a day trip to Füssen, as that may make the transportation connections easier and shorter.

Happy travels!

The link above will eventually take you to the Bahn schedule page, but this link will take you there directly.

Sometimes it might be a little faster to go all the way to Salzburg Hbf and take the RVO bus from there to Berchtesgaden, but there is a rail route from Freilassing, just across the river from Salzburg in Germany to Berchtesgaden. That route will allow you to use a Bayern-Ticket for 23€ (for one person, 27€ for two - new price as of 12/15). The Bayern-Ticket will cover your travel all the way from Fuessen to Berchtesgaden on regional trains for that price as long as you leave Fuessen after 9 AM on a workday.

There is a train leaving Fuessen at 9:05, with a 9 min, same platform change in Kaufbeuren at about 10:00. The train gets to Munich at 11:05. You'd have enough time in Munich Hbf to grab a sandwich at the food court before boarding the regional train (Meridian) at 11:44. Get off in Freilassing at 13:33. The train to Berchtesgaden leaves from the other side of the platform at 13:47 and gets to Berchtesgaden at 14:37.

A point of terminology which may make things easier for you to understand. It's not "the Eurorail." Trains in Europe are operated by:

1. National companies, like Bahn in Germany or Trenitalia in Italy
2. Private lines, some of which compete directly with the national companies (like Italo in Italy), and others which operate routes not run by the national lines (like Treno Nord or Circumvesuviana in Italy)
3. Multi-national consortia, like Thalys between France, Belgium, Germany and the Netherlands, or Eurostar between London and Paris or Brussels.

Trains in Germany are run by Bahn, and you've already been given the link to their schedule
website. Here are Rick's wonderful tips on how to use it. It's very handy for trip planning, as it has schedules for most of Europe. It will only have prices for trains that start or end in Germany.

In Switzerland you will be taking Swiss Rail (which operates some buses as well) or private rail lines. These will show on the Swiss Rail website, including the private lines (which may or may not show on other websites).

To buy tickets, you almost always want to go to the website of the company operating the train. Here's a guide to buying the least expensive tickets, from the Man In Seat 61 (a wonderful train information resource).

"it seems to only go through major cities."

To expand on what Harold said, There are about 5000 stations in Germany, about 1000 in Bavaria alone. That's not just in major cities.

To elaborate even further, usually high speed trains only travel between major cities, but regional and commuter rail covers large areas of the country. Think of it as the same hub-and-spoke system airlines use. You take the fastest train (Intercity Express or ICE in Germany) between major cities, then change to a slower train that stops more frequently to reach a peripheral, smaller destination.