I booked a flight ticket from Delhi to Chennai in October 2005 using makemytrip.com.
I had a few issues but finally it ended up well.
I will list down my complete experience.
I checked the websites of all the airlines and found that the fare was the lowest in makemytrip.com (The Airdeccan website quoted me a lesser fare but the flight for the day was booked completely).
I booked a ticket from Delhi to Chennai (Air sahara) through makemytrip.com 6 days before the day of journey. I payed through my credit card. (You can pay through DD as well but for that you should book the ticket at least a week in advance).
Two days latter I got a call from makemytrip.com that due to some technical problems they were not in a position to give me the Sahara ticket. As a alternative they offered me a complete refund/Indian Airlines ticket on the same day (Scheduled 1 hour later than the Sahara flight). I had no problems with the revised scheduled and so I accepted the Indian Airlines ticket. I immediately got my Indian Airlines E-ticket confirmed through the mail. The Indian Airlines E-ticket quoted a fare of close to 2k higher than the Sahara flight, but I did not have to pay the extra amount.
On the day of journey I showed my E-ticket at the Delhi Airport and the journey was hassel free.