I'm not sure exactly how these jammers work, but I would think there are two options on how you go about it.
1. Output a strong signal on the appropiate bands, thus blanking out any reception. Advantages would be that it would be relatively straightforward to produce, but it would consume a comparitively large amount of power, and would be prone to causing interferance in unrelated systems (ie aircraft sysems)
2. Output a weak signal more closely targeted to the frequency the mobiles operate on, to insert a pulse into the "handshake" between mobiles and the base station. This signal would only need to as weak as the signal recieved on the aircraft from existing mobile base stations. You would therefore have no problems for the avionics on board as the signal would be so weak.
If you have call waiting on your phone line with internet access you will have seen the effects of this, the call waiting "tone" stops the connection dead, as the computers cannot establish reliable connection, as your computer is reporting recieving a piece of data that was not sent, eventually this results in a dropped connection, then your phone rings
The futre for aircraft if mobiles become a larger problem would be something on the lines of the second system, unfortunatley it doesn't stop the phones interfering with avionics, as mobiles will tend to increase their output when faced with a weak / unreliable signal (ever noticed how the battery doesn't last as long where you have a weak signal). But what it would do is discourage passengers from trying to use their mobiles at all, as they would not work.