Is it possible to run more than two remote control trains on one track? My son has two passenger trains and a lego cargo train. We can get two trains running on the track using one remote. 

But how do you operate a third train?  We do have other remotes which came with each train. Do you use a second remote or do you use the number settings and just use one remote?
Each remote has 2 separate controls (one for "red" and one for "blue"), and 1 channel setting (choice of channel 1,2,3 or 4). Each train has an IR receiver which has 1 channel setting (again choice of channel 1,2,3 or 4) and two connections, one coded "red" and one coded "blue". From what you describe, you have two trains set both to the same channel (I'm assuming channel 1) but for one train you connected the motor to the "red" connector and for the second train you connected the motor to the "blue" connector. Doing so you can control both trains independently from the same remote, also set to use channel 1 (one with the left control, one with the right control). For the third train, set the channel on the IR receiver on the train to channel 2, and then take another remote and set it to channel 2 as well. Take note of which connector on the IR receiver you used to connect the motor to (the "red" or the "blue" one) and then use that color control on the remote to control the third train.

Alternatively, you can use a separate remote for each train, and assign each remote a different channel (e.g. 1, 2 and 3) and each train IR receiver also a different channel, matching to the channels you chose for the remote (e.g. 1,2 and 3).