I booked my tickets for home from Delhi on http://www.irctc.co.in for first time as this service has just been started where you can book tickets online for any train.
And despite charging you Rs. 25 extra as transaction charges, it also charges Rs. 11 from the bank used to book ticket. That amount is then cut from your account by the bank. I had to cancel my ticket of Thursday, April 13 and I has to book it again for Friday, April 14 because of our team party.
And when you cancel a ticket, Rs. 40 are again cut from your account as cancellation charges. And again, as money is sent back to your bank account, bank (and indirectly you) is charged Rs. 11.
So for booking, you have to pay Rs. 36 extra and for cancellation, you have to get away by paying Rs. 51. For a complete round from booking to cancellation, you have to shred total of Rs. 87 and that Rs. 11 funda is mentioned nowhere when I tried to search for it over the website.