My girlfriend and I plan to take off in October and see Eastern Europe, we came close to deciding upon a RailEurope pass but having read the advice on this site and elsewhere it seems the best option is to book individual train tickets online, in advance.
Besides the obvious expensiveness of the pass, it's also not valid for neither Russia or any Baltic states. While for rest of your Central-Eastern Europe itinerary point-to-point tickets will almost always bit pass price.
But let's look more specifically at each leg:
Moscow-St.Petersburg: most foreign visitors here would usually choose train (like famous "Red Arrow"), but if purchased in advance ticket for the flight will cost you considerably cheaper than "kupe" on one of the fancy trains.
St.Petersburg-Tallinn: there are no direct rail connection already for a few years, thus it's either pretty expensive direct flight or buses (frequent and cheap). Also possible to fly St.Petersburg-Riga-Tallinn with AirBaltic, usually they bit Estonian air direct flight fare.
Tallinn-Riga: most people here use buses since they are faster, but it is also possible to travel fully by train via Tartu-Valga-Cesis: you need to catch morning train Tallinn-Valga (6:46-11:35, 8.95 EUR), then in Valga there are connected change to train Valga-Riga (11:44-15:03, 3.75 LVL). Train to Riga waits for the one arriving from Tallinn, thus no need to worry about short timing between the two.
Riga-Vilnius: unfortunately, but no direct rail connection here, thus bus (or flight) is the only options. For crazy rail fans it is possible to go fully by rail from Riga to Vilnius via Rezekne, but that a bit illogical, will take a lot of time and cost more.
Vilnius-Warsaw-Krakow: from Vilnius there are everyday connection to Warsaw (11:40-20:10), due to gauge difference it requires train change in Sestokai. You will need to leave Lithuanian train and board polish ones on the same platform. Ticket will cost roughly 20 EUR. No need to book anything in advance, tickets are always available. From Warsawa there are already plenty of train options. Cheaper to use either TLK or InterRegio trains. Tickets for TLK train (including sleeper reservations) can be booked online -
https://bilet.intercity.pl/irez/Krakow-Bratislava: Polish Railways doesn't offer online sale of tickets for international route, thus you will have to buy this one already in Poland. One way ticket will cost around 50 EUR (+sleeper reservation). Also possible to purchase discounted international ticket here, but since those are in limited number, your chances to get one few day in advance aren't that good.
Bratislava-Budapest: relatively easy segment, direct ticket will cost 16 EUR, no need to buy in advance. Also possible to go via Sturovo-Ezstergom, will save you money and allow to take a look at nice town - Esztergom.
Budapest-Bucuresti: it's possible to purchase special discounted ticket online from MAV website. Those are called Fortuna ticket and start from 29 EUR. While full one-way ticket fare is 50 EUR, while return - 77 EUR
Bucuresti-Zagreb: here you actually have two major options: a) just do a side trip Budapest-Bucuresti-Budapest, so then you can go to Zagreb from Budapest (3 trains per day, app. 6 hours trip and 30 EUR ticket with no need to prepurchase anything); b) go via Serbia, thus catch overnight train Bucuresti-Belgrade (around 30 EUR for one-way ticket), while then daytime Belgrade-Zagreb (a bit more than 20 EUR).
Zagreb-Split: no problem at all, you can use train (
http://www.hznet.hr/timetable), bus or even fly.
Split-Ljubljana: here you again have two major options: a) from Split go back to Zagreb and catch direct train to Ljubljana from there; b) catch bus or ferry to Rijeka, catch train (twice a day) to Ljubljana from there.
Ljubljana-Vienna: there are discounted 29 EUR ticket available for this route (or 19 EUR from Maribor to Vienna), but you can also travel cheaply by using 28 EUR Einfach-Raus-Ticket from Slovenia-Austria border, while domestic ticket Ljubljana-border etc.
All of the above a kind of general notes concerning your itinerary, but if you have any further question - we are ready to give more detailed advice.