Trip report - solo female traveler conjecture on trains.
Booked all my tickets in advance on line OBB web site. It was confusing because you could do it in English until the payments page. I emailed and they helped complete, but it took a few days for each interaction. The trip Vienna to Prague and Budapest back to Vienna (in Nov) 2nd class (not crowded at all) was SparSchiene (a discount price based on? advanced booking?) 29.00 Euros. There were at least 3 direct (no changes) trains per day. BE SURE to arrive in Prague before 11 pm (when I arrived) or everything will be shut down (hard to get the coins to pay for the subway. Also in Budapest the subway closes at 11 pm. I felt safe each way (short trips) despite all the conjecture about safety.
The overnight (sleeper compartment) train from Prague to Krakow was very expensive because first you have to book 1st class ticket (something like 70 E, then you have to have a reserved ticket +15E, and you also have to pay 50E or so to be sure you have the compartment to yourself (they are small but workable, but it would be extremely awkward not to have it to yourself. The conductor took my ticket and said he would knock half hour before arrival. I locked the door and was not interrupted again (I think passport checks are less now due to EU, but they were checked when I was on the non-sleeper car segments of the trip). The train did arrive an hour late into Krakow (which was nice for sleeping, because it is only 6 or 7 hours).
Flying with small European companies whould have saved you a lot of money and time.