I want to price reail fares between Budapest and Salzberg, then, a couple of days later, Salzburg to Munich. I've been using the RailEurope site - it seems pretty comprehensive, but is there a site where I might get better fares?
Salzburg to Munich I would check out the DB web site. Budapest to Salzburg I would look at the Austrian Railways website (OBB?)
DON'T USE RAILEUROPE!
Sorry for shouting, but I mean it, certainly not for Salzburg to Munich.
There are plenty of trains between Salzburg and Munich, more than one per hour. The best deal is with a Bayern-Ticket, €20 for one person, €28, total, for 2-5 people. You can get them right up to train time at an automat in the Bahnhof. They're valid on regional trains all day weekends, after 9 AM workdays. The regional trains take 2 hrs, only ½ hr slower than express trains.
And, BTW, I wouldn't call RailEurope "comprehensive". They only show connections for which they sell tickets, and those are only the fastest, most expensive train. There are a lot they don't show.
Not only from Salzburg to Munich, but for any transport in the MVV (Munich metro - U-/S-Bahns, trams, buses - after you get there.
A ticket on an ICE, about the fastest train between Salzburg and Munich will run you €37,50 with a reservation, about $47 from German Rail, $60 from RailEurope.