A quick update, following my earlier post.

ÖBB
Austrian Railways now have their 2012 timetable available for booking online (although some further amendments may still happen).
An overview of key changes is available here (in German), with a map available here.

Sadly, it does seem the through trains from Munich to Zagreb have been discontinued (in order to avoid delays waiting for the through carriages from Belgrade?)

Euronights (EN) To/From Germany
Most of the EN trains to/from Germany (eg: Munich-Budapest, Hamburg-Wien, Köln-Wien, Berlin-Budapest) are now available for booking online at bahn.de.

However, there is as yet no sign of the Munich-Zagreb ‘Lisinski’ EN being available for booking online. There also seems to be a problem with the Berlin-Wien EN, as bahn.de doesn’t recognise that there are through carriages, and instead indicates a change at Breclav. Hopefully this is just a temporary computer glitch, as in the opposite direction, the Wien-Berlin EN shows up correctly.

Deutsche Bahn
This news article has an overview of the changes to the DB timetable.

Key issues are:

• A direct TGV from Frankfurt to Marseille, starting at end of March 2012.
• Various additional direct connections within Germany
• A new DB Express Bus service between Munich and Prague* (although this doesn’t appear in the bahn.de timetable yet...)

SBB
Swiss Railways now have their 2012 timetable available online (but don’t seem to have a news article giving details of key changes).

* Trains Munich/Nürnberg - Prague
There have been various questions about this in other threads, so just to clarify: there are trains between Munich or Nürnberg and Prague (not only the DB Express Buses). However, they are operated by CD and ALX (not DB), and don’t always show up easily in the bahn.de timetable.

The 2012 timetable seems to be as follows:
Munich – Prague:
ALX355/EX355 Dep 09:01, arr 14:51
ALX351/EX351 Dep 17:02, arr 22:51

Prague – Munich:
EX352/ALX352 Dep 09:57, arr 15:03
EX356/ALX356 Dep 17:07, arr 23:05

Nürnberg – Prague:
ALX357/EX357 Dep 06:01, arr 10:51
ALX353/EX353 Dep 14:05, arr 18:51

Prague – Nürnberg:
EX350/ALX350 Dep 05:07, arr 09:56
EX354/ALX354 Dep 13:07, arr 17:56

It is not necessary (nor, AFAIK possible) to make advance reservations on these trains.

For travel from Germany to Czech, for any of these trains leaving after 9am (or any time on weekends), a Bayern-Bohmen ticket costs €34 for up to 5 people, to travel from Munich or Prague, as far as Plzen in Czech. From Plzen to Prague is 147Kc per person (~€6). It should be possible to buy this ticket on the train, once it has entered Czech (and although it’d be better to pay in Kc, they’ll probably accept euro. If you buy the ticket from the conductor before the train reaches Plzen, you can't be accused of travelling without a valid ticket). For two or more people travelling together, this is likely to work out cheaper than the DB Express Bus (and doesn’t need to be booked in advance).

By changing in Schwandorf, it is possible to use the Prague-Munich service to reach Nürnberg (or vice versa). However, note the Bayern-Bohmen ticket is only valid on ‘local’ trains – not ICEs (nor the Express Bus).