I have booked atleast 4 times through this web site and once a hotel booking.
Flight Booking experience:
Everytime I was about to book, I used to check the rates from the original website and found it to be the same. Except once when their air deccan tax amount was reflecting the old amount and I ended up paying Rs. 100/- more for two tickets. When I mailed these guys I didnt get any refund or reply to my mail. This was my only bad experience.
Their comparison page is pretty good. Especially the slider which u can use to select the amount upto which you are looking for and it automatically removes those flights which do not fall in that range without refreshing the page all over again.
Twice I had to get in touch with the customer care and mailed them as I was not able to get to their MTNL/BSNL numbers. As mentioned in their FAQs I got a reply to my mail within 4hours of me sending the mail.
Hotel Booking experience:
Once I booked a hotel in Trivandrum thru this site and I never got a confirmation. When I contacted the hotel people, they said that their rates were different and it was a little higher than that mentioned in the site. Finally I got a mail from yatra which said that they regret for the inconvenience caused as my booking did not go thru due to some technical reasons. Not sure what that meant. But good they intimated me much earlier so we called the hotel directly and made the booking.
In summary, this site is not bad compared to others like cleartrip.com. As long as the rates are cheaper than that mentioned in the airline websites, we can go for this. Right now they do not charge a cancellation fee of Rs. 250/- as they have just started. But once they start charging, we may need to think twice.