I have developed probably the largest, most detailed and most demanding (hardwarewise) RRT3 map ever, the "Great China" now for a long time. The game has been surprisingly stable even under the most extreme testing: 200 cities, 600 trains, absolutely countless resources moving from one place to another. So stable, actually, that I have only witnessed 1 or 2 crashes ever, and even those may have been caused by other issues in my computer.
But... There is at least one serious bug I face in every long test run. The others are rare and only seem to happen occasionally.
It's about train routing, and it happens after I start electrifying some of the track. Rarely, but still sometimes an electric train suddenly moves to a random other place in the rail network without any apparent reason. To a place with no electricity, that is: so, it gets stuck there. The only way to resolve the situation is either to build an electric track to that place, or to replace the engine with a steam or diesel model so that the train can "return home". This may have something to do with changes in the original track section - for example, changing the original line or its features like water towers etc. Anyway, it's a nuisance expecially when one has 500+ trains running (can't easily find the lost train)...
When you have really lots of track and trains, RRT3/TM can kind of freeze when removing water towers and service sheds. It can then take a long time before anything happens again. In extreme, very rare cases, the whole game can freeze/crash. Probably a memory allocation problem.
Electrifying long sections of track sometimes leaves small sections of track unelectrified, requiring one to check and re-electrify the whole section.
Last, a relatively rare, nasty bug: sometimes the routing just doesn't work. Then the train simply doesn't use the shortest, logical route, but instead wants to take a "long route" - which in China map's case can mean a VERY long route... This is probably related to another bug related to especially electric (but also normal) routes sometimes being unusable when there are many bridges and/or tunnels in the route.
AMD Phenom X6 1090T @3.9GHz, 8GB DDR3-1600 RAM, Asus Crosshair Formula IV mb, Radeon HD7870, PNY SSD, M-Audio AP192, Windows 7-64, Railroad Tycoon 3 1.06. & TM, Train Simulator 2013, MSTS + many add-ons, Trainz!