I have looked at the German schedules on the web in Germany,but will buy the tickets upon arrival in Germany next week. We are traveling by train from Munich to Vienna and then return back to Munich 2 weeks later. Also a trip by train from Munich to Rothenburg and then back to Munich. Possibly a train-bus trip to Neuschwanstein and return to Munich. What type of ticket should we buy? What would be the cost of each or would the German Flexipass be a better deal? Does this type of pass cover a trip outside of Germany as we are traveling to Vienna? What is the difference in 1st and 2nd class as far as comfort, etc.?
Thank you for help about the train. I already have the website for the German train system,but need more help.

You can try your itinerary at :
www.railsaver.com
to see if a pass would be cheaper.

Note that Eurail passes MUST be bought from the US, so that ship has sailed... There might be passes available to buy IN Germany, perhaps another poster will have an idea.

The DB website provides you with the cost of the journeys within Germany.

If you stay overnight in R'burg and Fussen, you'll have 6 days of train travel, right? That's $340 for two 2nd class german rail flexi-twin-passes, the cheapest pass option. Regular fares for two add up to about $380-$400 on the fast trains. However, daypasses on the regional trains are a much better option than either of the above. 6 days at 21 Euros (weekday travel) or 28 Euros (weekends) will cover both of you, so you're looking at anywhere between 126 Euros and 168 Euros (if you travelled on Sat or Sun's only) total for two. The regional trains will add about 1/2 hour to your transit time betweeen Munich and Salzburg, about 1 hour between Rothenburg and Munich. You sacrifice nothing by using daypasses going to Fussen because the Regionals are the only trains that go there anyway.

All weekday travel must begin after 9 am on these daypasses. Weekends, any hour. Buy your daypasses in advance at any DB counter in Munich.

I would use these, then just buy regular tix for Salzburg - Vienna.

Thanks to both of you for your help. The regional train sound like a much better deal even though the trip may be a little longer in time.

One thing to keep in mind. the German rail has several unadvertised specials every summer, so ask if there are any specials to your locations before you purchase your tickets. They, normally do not look for these specials without being prompted. Some specials even include hotel accomodations. I have used this method (nix hotels) going to both Paris and Hugary!