2. Expect the train to be late, unless you are boarding the train at its point of origin. Our train from Istanbul left exactly on time but lost a couple of hours along its route. On the way back to Istanbul, we boarded the train about halfway through its journey and it was half an hour late. You can ask the train station employees when a certain train will be arriving, and they just might know the answer. Then you can adjust your (and your kids') expectations as necessary. Because hoo boy, if they are anything like our kids, they will be beyond antsy to get on that train.
3. Be ready for slightly cramped conditions. Honestly, the train compartments were bigger than I expected them to be. There are a couple of hangers on the wall, a sink, a mirror, and a few cabinets under a table. But there's not a lot of space to play, unless it's on a seat or bed. (Inexplicably, there is a fridge in one of the cabinets, but it doesn't seem to operate.)
6. Consider that the journey could take a lot longer than you think it will. Like, A LOT. Our train back to Istanbul was supposed to arrive there at 1pm. It didn't get there until a little after 5pm. Sometime around noon, when it was already running late, our train lost power and sat motionless on the tracks for a long time. The AC stopped working, too, so it was an uncomfortable, uncertain delay. Bring more food, more activities, and more patience than you think you'll need. And don't schedule anything like a plane flight too soon after your expected arrival time at the train station.
7. There are two bathrooms on the train. One is a Turkish toilet. The other is a Western style toilet. My preference is for the latter, but as the journey wears on, the Western toilet is going to run out of tp and paper towels and cleanliness first. So you might end up using the Turkish toilet anyway.
8. Some good activities to bring include: audiobooks on an iPod Shuffle that you can listen to easily in a cramped and sometimes dark space (instead of reading an actual book that takes up space and requires light to see), lots of snacks, an iPhone (and an extra battery), and cheap toys you bought at the dollar store (or its equivalent wherever you live). The girls had a little backpack full of dollar store flotsam and it was a hit with the other kids on the train, too. They all took the toys to that empty compartment I mentioned earlier and played for a couple of hours. Since it was just dollar store junk, I didn't care if any of it got lost or broken or carried off by some random Turkish kid. Bliss.
We had a great time on our overnight train rides with our kids, even though one of the trains was delayed so severely. It was such an adventure watching the Turkish countryside roll by.