How to prepare for very long train journeys?

In addition to the sound advice from victoriah, here are also a few more points to consider:

• Some trains have power sockets that you can use, so bringing an entertainment device (laptop/netbook/tablet) stocked with stuff to read/watch might be a good idea. Bringing a power strip will also make you popular among other travellers, if power sockets are in short supply.
• If you expect to be sleeping on the train, make sure you schedule a few alarms on your mobile phone before each stop -- although train stops are usually announced on the intercom, you might miss it if you are overly tired from the journey.
• A sleeping pillow like the ones usually brought on planes can help a lot and reduce the possibility of falling over your neighbour.
• Probably goes without saying, but when travelling in countries where train theft is common, secure all your belongings (at least your handbag, or equivalent) so that they cannot be snatched without waking you up. Best is to put your most important belongings (wallet, mobile phone, keys, tickets!) in your trouser pockets. Otherwise, you could just wrap the strap securely around your hand, and put it in a position that will be difficult to open without you noticing. You may also lock it with a padlock, and even use it as a pillow (thanks for the tip, victoriah!)
• Some trains are cold, so a warm thin blanket will be much more comfortable than staying with your jacket all the time. Remember also that body temperature drops while sleeping, and without something to put on, it makes for very awkward sleeping.
• Take some "comforting" medications, such as anti-diarrhea pills. You never know, and train toilets are not always comfortable to use (some trains in Bulgaria used to have squat toilets until few years ago, for example).
• Take some toilet paper. Trust me on this one.

Food

Make sure to buy some food before you go. My favourite train snack is pistachios, because they take a while to eat - chews up time ;) Also make sure you have plenty of refreshments, especially caffeine if you're the sort of person who needs a shot when you wake up! Some trains (Russia) let you get off at stations and there are dozens of people selling cheap food and drink, but this is less common in Europe. And DO share your food with others - it's a good bonding activity, and you get to try out some of their food too!

Seating

Firstly, if you're in a cabin/carriage with just seats, you'll want a window seat. If you're ok with being a jerk about it, when the adjacent seat becomes available, you could put your stuff on it. This gives you an extra seat to use when you sleep. However, this will depend on seating numbers and whether you can change or not as well. In a train from Berlin to Krakow, a Brazilian girl and myself hunted through the train until we found an empty cabin. It had 8 seats facing each other. We each stretched out on four seats, and went to sleep. This worked well except for a random period from 4-6am when some kids came in and used 3 of the seats for two hours, and then they were gone again.

Security

If you're travelling alone, this is even harder, but make sure to keep your possessions close by, if at all possible. Keep you wallet in your clothes, and if you're comfortable doing so, perhaps use a daypack as your pillow, with your valuables inside. I try to lock my leg through a strap on my pack if possible, for extra security. Consider using one of those wire-mesh security wraps for your pack - makes it much harder for someone to get in while you're asleep.

Entertainment

If you're in a carriage with others, it's chatting time! Everyone you meet has a story, find out theirs! And this is the best part - even if they're speaking in a foreign language, make it a game to figure out words - even if it takes you an hour to work out where they're from, what does it matter - it's a LONG train ride! Perhaps get them to teach you some words in their language - count from 1 to 10 etc. If you have playing cards, these are fantastic to use, and cheap.
Also consider books, a Kindle, netbook - whatever you use to entertain yourself while others are busy, or if there are no others around. Quite often travellers are keen to see your photos, and if you're as snap-happy as me, you can easily spent a couple of hours looking at each others' photos. By the end of the ride, you may have made a friend, found accommodation, or know a lot more about your destination, including locals' secret tips!

Having done London to Singapore by train¹ I know a little bit about long train rides.

Victorah and mindcorrosive covered most things already. Here are a few more random thoughts:

• If your friend is lucky he gets one of the older compartments with 'pullable seats'. There are usually three seats on each site and you can pull the seats towards the center of the compartment to get one huge flat area (see photo) where you can sleep much better than in a seat. These type of seats used to be pretty common in Europe but are less so now. However I've been in such a compartment in the last few months someone in Eastern Europe, so they are still around.
• In some trains you can get hot water for free, so bring a cup and a few tea bags.
• If the toilet is just a squat toilet and you can not remember the answers to 'how on earth should I use a squat toilet?', (which is even harder on a moving train), look for another WC, most carriages have one each of the two types. The first class carriages always seem to have western ones.
• Obviously, bring something to read, audio books, podcasts or just music to listen too.
• Bring playing cards or another small game and play it with fellow passengers. If not everybody speaks English it can be fun to teach/learn the rules of the game.
• The enjoy-europe.com website has a lot of information about Night Trains in Europe

¹ Okay, I had to take buses in Cambodia and I also did stop in places on the way.