I have a ton of questions, but I don't even know where to start. To those of you who have done the journey, what is a good starting point for planning?
Personally I didn't plan much, just went with the flow, but that depends on how much freedom you have.
Work out how much time you have. Bear in mind that a Russian tourist visa is 30 days, but you can get a Business visa for tourist purposes (I had zero problems) and that's valid for 60 days, multiple entry.
Work out your budget. Hostels are pretty cheap in most cities. However, Moscow and St Petersburg are expensive - European expensive. Starbucks in Moscow (I use it for my price gauge) was frightening!
Work out what cities you want to stop off in. You do NOT want to just train from end to end. Remember, Russia is BIG. Russia is LONG. Russian trains are SLOW. There are frequent stops - although they are almost to the minute reliable, in my experience. As an indication, Moscow to Novosibirsk takes 52 hours.
Work out what class you want to travel in. Platzkart is fun to do for some segments - you get beds in a 54-bed carriage. It's social, you meet lots of people. Kupe class is 4-beds in a cabin. More secure and quiet, but if you get crappy roommates, it can suck. Work out if you want top or bottom bunk - the price varies. Also some trains (Between St Petersburg and Moscow, for example) can also offer merely seating class - but you always seem to get 2 seats or more to yourself, so can sleep quite comfortably, although it's a lot less secure, and you quite often get drunken soldiers or louts keeping you awake.
Work out what sites are near each city, and therefore how long you want to spend there. As a starting point, Moscow doesn't near nearly as much time as St Petersburg. Also be aware that if you stop in Irkutsk, you'll want to go to Lake Baikal, which to do properly you'll want three days, minimum.
Work out a rough guide for length, activities, price and see if this fits into your visa.
Look at flights in and out of start and end points (I assume you're not going both ways on the train).
Look at visas for Mongolia and China - but you can pick these up in Irkutsk, Russia quite easily (Mongolian visa takes 2 days, or less if you're prepared to pay).
Do you want to go into the desert in Mongolia? It's a minimum 4-5 day tour from Ulaanbaatar.
Assuming you finish in Beijing, allow time to travel there as well.
Put a couple of buffer / rest days in here and there. Although you will get a lot of resting time on the trains.
Learn the ten most useful phrases. Hello, thank you, train station, bus station "where is x", your country in Russian, and "what time is x" is an excellent start.
Decide if you're going to buy all your tickets outside the country. Personally I wouldn't, it gives you more flexibility and I've never had a problem getting a train ticket even the day before in Russia - well, aside from in Irkutsk after 7pm.
Get invitation, get visa, buy flights.
Go to Russia, and enjoy it!