Irctc users can select their preferred seat or berth whil booking in nget.irctc.co.in.
It is in development and expecting this to be completed by august 15th 2014.
Recent news says, in the new budget they have allocated money and feature to select seats/berth while booking.
In current system, users cannot select the berth or seat they want. Automatically system checks and selects the seat.
Dont know how they are going to add this feature to the current system. This change is going to be in the new nget irctc eticketing system.
Lets wait and see the new system.