Picture of Miniatur Wunderland Car System Equivelent
Have You heard of Miniature Wonderland?  It is the world's biggest HO model railroad and is located in Hamburg, Germany.  They have a massive car system and the whole thing is full of secrets of how they did it.  They have a article on their site, but it's not that descriptive.  Luckily, I took the time to look through their descriptions and figured out how I think it was done.
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Step 1: Materials

Picture of Materials
Here is what you will need.

Faller Car System:
Vehicles of your choice
Any Other Accessories You Would Like (You can make your own after completing this article)
If you are reading this after 9/13, get the Car System Digital 3.0
At the time of writing, the digital system 3.0 is not available.
Beware the links above are in German.  Click the USA flag at the top to get it in English.
There may be more items you will need as you go through this article but that is all that is needed to get started.

Step 2: Set Up The Sensing Rig (optional)

Picture of Set Up The Sensing Rig (optional)
Unfortunately, I did not write this step, I found it.  So do the following step.
You can also skip past this step and do step 3 or do both.

Step 3: Start, Stop Rig

Picture of Start, Stop Rig
Now what you are going to have to do is put a network of stop rigs, or electromagnets around the layout so you can stop the cars.  They will sense the magnet and shut off the motor.  I would recommend wiring them to switches on a main control board so you can flip a switch and stop each car.  They also sell them directly.  This can Also replace step 2.

Here is a video I found with a very small car and how to stop it.
Or, if you want to pay for it, you can get the PC Controller and save the hassle.