Originally Posted by stut
I personally found more to do around Ljubljana than Zagreb (particularly as you have the possibility of trips to Bled and Bohinj).
However, I would just leave it flexible. The trains don't get that packed, and the fares are relatively low, so I wouldn't bother booking those journeys in advance, just see where the whim takes you!
I agree unless you're taking one of the night trains between these cities. Many of the trains only have 1 or 2 cars of couchettes, and can be booked far in advance, particularly in summer. DO NOT book, however, until arriving in the Czech Republic (or at least Europe) -- prices are much cheaper than in the USA.
I did a similar trip in '03, travelling from Prague - Warsaw - Krakow - Budapest - Venice - Vienna and found the train a great way to go.