After reading all the negative reviews I must narrate the good experience I have had with makemytrip.com . I was abroad when I booked domestic tickets from Mumbai to Delhi for myself and a friend. We chose to travel Air-India (domestic sector) since we were arriving at Mumbai from abroad and it saved a change of terminal. During the transaction I gave a local Delhi No as contact tele. About 30 min after booking (and money debited from my creditrcard), a person from makemytrip called up my friend at Delhi and said that the tickets which we had booked were not available. However he offered to put us on the next available flight (Air Sahara). They did so and even paid the difference in cost (total about Rs 1300) for both tickets. Thje tickets were delivered promptly within 3 days to the address in Delhi.
However on another occasion, they did not list the flight on which another website (yatra.com) was offtering lower rates. Both these events are of Sep-Oct 06 and so very recent.
Their response on toll free Nos leaves much to be desired. Maybe they can improve that.
Quite often when one chooses a flight and clicks to proceed for ticketing, the message of this flight is no longer available at the fare you have chosen appears. Maybe they require to pay more attention to updating their database.