It's the sort of setting where you could expect to find a lot of high-powered corporate executives, organized crime figures, and European aristocrats. And its traditional route would take it across a lot of boundaries in Balkanized Europe.

So...

(1) Does it still exist in Shadowrun?
(2) Who would own it?
(3) Who would use it?
(4) Would it follow its traditional route?
(5) What security measures would it have?
(6) How would Shadowrunners get access to it

And optionally...

(7) Whodunnit?

yeah, except now it's a launch point for space planes to Z-O and it's on top of Mt. Kiliminjaro.

You could always try the Grand Tour if you're looking for something more political/intrigue.

...last I recall, much of the Balkans are kind of a Merc vs. Muslim free-for-all.

Now a VR recreation, that could be a different story with some interesting twists.

My quick thoughts before I go to sleep.

(1) Does it still exist in Shadowrun?

It does if you say it does. Canon? Who cares?

(2) Who would own it?

Dunno, no books handy to use as the basis of assignment.

(3) Who would use it?

Jet-setting, sub-orbital flying, high powered mucky muck corp types take the train when there's enough time to enjoy the finer things in life.

(4) Would it follow its traditional route?

I don't know its traditional route, to be honest. I'm more familiar with a loose concept and story of what the OE is like than I am with it itself.

(5) What security measures would it have?

Well, the train I used in a game a few months ago had satellites monitoring it, it had sensors in the track to report stoppage or track problems, it had a security mage and security decker in the main engine car, and the stations all had high rating MAD and 'ware detectors, as well as requiring slotting credsticks at multiple points to get on. The security was based on the idea that once the train was moving, it didn't have to be all that secure, because you're keeping the "bad guys" from getting on it in the first place.

Tell that to the mark they geeked.

(6) How would Shadowrunners get access to it

Send the mage. No 'ware, no weapons, spend lots of money on a fake ID and you're golden. There are ways of getting the others on, of course.

LMFAO! Our group did an Orient Express run recently and you just reminded me of it.
We where taking a trip from Vladivostok to Istanbul. Naturally during the run there was a murder so they rest of my team went about trying to find the culprit as they where pretty big suspects themselves. My character got sick of all the noise outside in the hall, he was trying to have some quality time with his assistant, so he eventually just sent a Force 8 spirit out to kill the passenger my team was talking to at the time. I had my suspicions but we had no proof. I frankly didn't care, luckily I was spot on and it was that dude, a shapeshifter that did it. One amusing close range firefight later and we bagged our cat, err man.
My character never did leave his cabin that entire trip.

Recently I used the Trans-Siberian scenario as a form of Intro/testing ground for potential shadowrunners before the campaign really began.

The Johnson contacted each player in Moscow, for a meeting in Vlad City in five days. He provides each with tickets to the train and specific restrictions about what magic and weaponry to bring along the ride.

Once the players are on their way, it quickly becomes apparent that they each have a corresponding NPC rival passenger onboard. The johnson sets an individually task to each player that must be completed by the time the train reaches Vlad city in five days. The corresponding shadowrunner who succeeded would then prove worthy to the employer.

In the case of the mage, he was competing to steal a potent fetish from a rich talismoger passenger. The decker had to be the first to access the security vault onboard the train. The St.samurai/Razor guys had to find and bring back proof of a rare para-creature during a half-day layover at Irkutsk.

Obviously, the players quickly solidified to help each other in their respective tasks, but there was a great deal of intrigue as NPC's got knocked off and the players wheren't sure "whodunnit", or if they were going to be next.

I suppose you could modify the scenario to tougher shadowrunner by increasing the amount of Red Guards onboard; adding more sophisticated security measures such as spirit or camera monitoring; or, to be really nasty, you could set opposing tasks to certain player shadowrunners.

There is great deal of information in the 'Smugglers Haven' sourcebook, but when in doubt use RL sources. There is lots of stuff on the web about the real Transiberian rail, such as maps and photos that you can use.

How about the circa 1889 Orient Express as a mobile alchera/astral construct (a ghost train, of sorts) complete with passengers and employees who may or may not be real? Really, ATGMs aren't much of a threat to a train that possesses Immunity to Normal Weapons. The big problem comes when it vanishes in mid-route leaving the meat passengers with no train and probably no track.

Likewise, heavy magical protection (high force elementals or Free spirits and quickened naval-scale armor spells) and some high-tech mundane protection (turrets, cruise missiles, a spy satellite uplink with indirect targeting capabilities, snake-spine tentacles with hull cutters, NBC sealed cars). If you are using SR4 ally spirit rules you can make it a hybrid-merge to gift it with Immunity to Normal Weapons or you can just have a Great Form Plant Spirit possess it for both Immunity and Regeneration.
The chances of even the most powerful warlords taking down a train that is so equipped are relatively low.

It is certainly possible to make the train unassailable. Enchanting the cars and the track as a single homunculus/prepared vessel, equipping it with naval armor, and summoning a double-digit force regenerating spirit into it should be more than enough to ensure that the passangers will be delivered to their destinations both safely and on time as it prevents both attacks against the track and engine failures (since the whole thing would be one giant regenerating spirit the track would heal automatically and the spirit would be able to move the train along the track in the same way that a normal person flexes an arm).
But, any such solution would be very expensive and not at all cost effective.

People have already said what occurred to me- the Transsiberian rr. Exotic with out having to go through a war zone. people could take it becasue of the sense of adventure- the way rich kids go slumming in the barrens, more mature people go
to see the wild lands where maybe evil shamans plot and summon up storms. Of ocurse they do that in a well protected train loaded with luxuries.

For a run, look at the James Bond movie From Russia with Love.
Another

I would expect that movie gives a good example of what you could get with small cabins along one side of the car with a corridor running the length of the other side. I did that sort of ride once with my family years ago. Private room and toilet. and it was surprisingly comfortable.

High level muckety mucks might have a private, luxury car, at the end of the train.

The other way might be instead of a train, zeppelin.

VR recreation is a great angle.

There was a run on the Orient Express that the #S-Run Community did years ago. As I recall it ended rather messily.