Question: Rail Europe seems to essentially double the price of a train ticket (point to point). The German site is more reasonable, but I missed a window to get a really affordable ticket (Munich to Vienna roundtrip). My question is, is it usually cheaper to buy it there? Or do the prices to continue to rise and the date gets closer?
Any advice is greatly appreciated.

no and yes. tickets at stations i think are pretty much a set fee for trains like that. But online there are SPAR fares - discounted restricted tickets for trains involving Germany. Not always available and reltaveily few in number.

So to say money go to www.bahn.de and see what's up - full fare you can always buy at the station in Europe.

Doubling is hyperbole but RE often sell tickets at significantly more than you'd pay in europe - but like you say you should check them because they do also have the occasional special. Like $16 Paris-Amsterdam Thalys tickets they were selling last summer.

Plus with RE you'd have to pay an $11 seat reservation fee if you wanted a reservation (not needed IMO) and a $15 order fee and a $15 mailing fee on top of the ticket price.
(RE does not include seat reservations in the price unless the train requires reservations and this one i believe does not.) none of these fees are incurred online or at stations in Europe for this ticket.)

Best rail advice I've found is from BudgetEuropeTravel.com. Call their 800 number. They are extremely knowledgeable and helpful. They also have an office at the Munich train station.
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one word: FLY

PalenQ is correct. DB is not like the airlines. The normal fare is set; they don't keep raising it as you get closer to flight times. What you see on their website is the normal fare you would pay at a ticket window over there.

DB does, however, have some limited number of special fares that do sell out. These fares are shown as "savings fares". What was the really affordable ticket that you missed out on? DB is running a promotion called Europa-Spezial - Munich to Vienna for €29 each way. That fare is valid for three trains a day; surely they aren't all sold out. You can access these fares by going to http://reiseauskunft.bahn.de/bin/que...ogram=esi&. Select "München" for From and Wien for To, and put in your date and time.

If those fares on your dates are sold out, and you are looking for a round trip, try for a Sparpreis fare. If you book 3 days in advance, it is 25% off the €144 RT. If you also stay over a Sat. night, it is 50% off. That's €72 - €112 RT.

You can't buy the €29 Europa-Spezial tickets at a ticket counter over there, only online. You might be able to buy the Sparpreis tickets at a counter, but if you wait until you are there, they might all be sold out.

off the €144 RT. If 144 euro is the standard price, or about $190 then you may want to investigate the Austrian Railpass which gives you three days of unlimited travel in Austria for $136 p.p. in 2nd cl or $199 in 1st cl - and use the Bavaria pass to go to Passau and the Austrian border or the normal Munich-Passau fare can't be too much.
Depends if you could use the third day in Vienna area, day trip to Melk, Danube cruise, Krems, etc.
If you are traveling much more by rail in Germany then you could look at the Austrian-Germany Eurailpass, which starts at 5 days of unlimited travel in a 2-month period i believe - a flexipass - for $257 p.p. saverpass in 2nd cl or $302 p.p. in 1st class - with versions up to 10 days possible.
Thus if you were taking a long potentially expensive train trip in Germany as well it could be a good deal...especially if you just want to be able to hop any train any time and not have to scurry for SPAR fare restricted type tickets, which, though if you can get them for 29 euro are a real bargain.

For the record, the normal Munich-Passau fare is €28,30 pP, so the Bayern Ticket at €19 for one person or €27 for 2 to 5 people is a better deal. The fastest route (2h12m) to Passau is a direct Regional Express (RE), so you would probably be using the same train with either a normal fare or a Bayern Ticket.