This is the charger I'm using:
http://www.himotoracing.com/product/electronic/electronic_027/images/electronic_027_01.jpg
That is a balancing charger, and usually, three of the four wires are connected to the three positive terminals of the three cells in an 11.1V battery pack. The other lead is connected to the battery pack negative terminal, as shown here (the wire colors MAY NOT be correct).
You have to know which wire in the charger connects to which cell in your original pack in order to use it with a different 3 cell battery pack.
It is possible to determine those connections from your original battery pack using a voltmeter. The voltages on the individual wires coming from either battery pack will have voltages of roughly 4, 8 and 12 volts, measuring from the negative terminal.
Connect those leads from the charger, in the same order, to your new battery pack.