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Hi I am wondering whats the best of travelling to Prague from Munich ?
We will going the last week in november but would like a few days at Nuremburg along the way
Is it best to pre book or just get them at the station ?

Many thanks

Options depend on a number of people traveling:
In case of 3> passengers, probably, the best type of ticket for you is Bavaria-Bohemia ticket. Up to 5 passengers can travel with such ticket as much as they want within whole Bavaria and neighboring regions of Czech Republic (in your case the farthest point ticket valid for - Plzen). It is valid for direct Nurnberg-Prague ALX train or any other combination of regional trains (for instance, change in Schwandorf for Munich-Prague train in the evening). Bavaria-Bohemia ticket can be bought any time, even 5 minutes before train departure. For Plzen-Prague part of the journey you can buy tickets either online (https://eshop.cd.cz/search.aspx?lang=E) for the same train you will come on, on board (with small commission) or get off the train and buy tickets at the counter, afterward you can simply board next train to Prague (Plzen-Prague route offers a lot of trains during the day, so you won't wait long for the next one). Ticket Plzen-Prague cost around 150 CZK (+ group discount in case 2 or more passengers traveling)
From Munich to Nurnberg you can as well use Bavaria ticket (up to 5 passengers cost 28 euro). Regular ticket for one person for regional train cost 20 euro, so Bavaria ticket will save you quite a lot in case you travel with someone. 

Other option: discounted "Europe Spezial" fare, Nurnberg-Prague starts from 19 euro per person. Those tickets you need to purchase in advance online from DB website - http://reiseauskunft.bahn.de/bin/query.exe/en?newrequest=yes&protocol=http:& (such tickets can be used also on direct DB buses Nurnberg-Prague), with such tickets you won't need to have any hassle with purchasing Czech domestic tickets, so it is better option for single or 2 passengers.

The info provided by the Administrator is spot on. We just travelled (3 of us) from Munich to Prague by the ALX 355 on 16th July 2011 and I don't think there could have been a better way.
The Bayern-Bohemia ticket was bought (group ticket for upto 5 persons) was bought at the Munich Central Station from a MVV Ticket Vending machine, which was not a challenge.
This ticket is valid till Plzen, at Plzen we bought a group ticket from the conductor on board the train itself for Euro 19:60. The total journey costed us less than Euro 60.
ALX 355 is the only train without any change overs from Munich to Prague and lasts 6 hours, I tried hard for a faster route but could have saved only an hour probably if I did a train and bus combo, but than I didn't want to risk a changeover (of about 10mins) with baggage.
The train has 3 carriages for Prague and are at the end of the train so are actually the first three from the station side as you walk into the platform. There is no seat reservation for this train and there are ample seats. The 2nd Class is as good as the 1st class, so no need to spend more.
Remember to carry some food from Munich itself, water is a must, as the stops on the way are short and there isn't anything on the platforms on the way.

Sodeep, thanks for sharing your experience
Definitely Bavaria-Bohemia ticket is the best option in case a group or a family travels together, such ticket almost always can beat any special offer.

The Bayern-Bohemia ticket was bought (group ticket for up to 5 persons) was bought at the Munich Central Station from a MVV Ticket Vending machine, which was not a challenge.

You did exactly the right thing, ticket machines in Germany are rather easy to use, while by purchasing the same ticket from the ticket counter you'll have to pay extra 2 EUR, which is not a lot, but still no need to pay more. So for anybody planning to use this or similar Lander tickets we advise buying them either from ticket machine or online, then you won't need to pay those additional 2 EUR.

ALX 355 is the only train without any change overs from Munich to Prague and lasts 6 hours

Actually, as of now, ALX/Ex 355 ("Albert Einstein") is not the only direct train. There is also almost a mirror train in the evening with app. same total travel time - ALX/Ex 357 ("Franz Kafka"), 17:02-23:00. Same thing on the route back - two direct trains per day (morning and evening).

...at Plzen we bought a group ticket from the conductor on board the train itself for Euro 19,60

Hmm... interesting. So you actually payed in EUR? Previously you could pay in EUR only at the station ticket counters, while now, apparently, you can do it on board as well. Good to know.
Also one small correction, 19,6 EUR corresponds to app. 470 CZK, which looks like the sum of three full fare adult tickets Plzen-Prague + 30 CZK for buying on board. So we afraid you actually didn't receive the group discount  Probably some misunderstanding between you and conductor, since group ticket for 3 passengers Plzen-Prague cost 296 CZK, if bought from the ticket counter, or 288 CZK, if you buy it online from CD eShop. But anyway you overpayed just around 140 CZK in total, which isn't that much, so not a big deal.