Another vote here for Cleartrip. I've booked Goa (Thivim) to Bhopal and then Bhopal to Chennai... and recently thought I'd best do the return leg to Goa and booked that from Kerala. I think it works out at around RS100-200 extra to do it via an agent like Cleartrip but anyone who has ever stood in a booking queue will know these are roops well spent
I've just had to re-schedule my Kerala-Goa leg for a few days later and the cancellation was simple at a cost of about RS100 on the refund.
If you do book from here, all the booking systems close from about midnight til 6am India time so I usually do this about 1am here when they have warmed up the system
A link I use to check trains:
http://erail.in/
And Indiamike is an absolute godsend, so much info on there it's unreal. Helped me plan my south India itinerary and I'll be back on there soon to plan the north