Recent days flight travel has become more common for all people in India as there are many flights offering low price for travelling in their flights. More over flights are one of the fastest means of transport where one can be assured of reaching the destination on a calculated time without major set back. Some of top flights booking sites in India are as follows.  This site offers search for flight, train and hotels, get fare alerts. Even has a mobile search application.  This site offers you cheap domestic and international air tickets. It also has a miles program, wherein you earn miles for every ticket you purchase. Recently they came up with a system on how people can redeem those miles [How to Redeem Yatra Miles]. 
This is one of the first travel aggregator sites with fare trends which I know of. This site is very fast and user friendly. Brings you flight, hotel and bus deals from several sites at one place.
 This site offers airlines ticket search for domestic flights in India. They have integrated this with Yahoo Messenger so you can your friend can plan for a travel and choose flights together. [Yahoo Messenger India Flight Planner]. They also have a neat “my fare alert utility” which allows you to create an alert for flight fare for a certain date. As soon as the price falls below your set limit, it can alert you via email or your yahoo messenger.  This site offers air (domestic and international) flight reservations. It also gives you the fare price graph so that you get an idea on when the prices are low and when high.  Apart from the flight search interface makemytrip gives users special offers combined flight hotel search for added discounts and excellent holiday packages. The 'Plan your trip' section gives users useful links like Holiday ideas, Destination features and Driving directions. Features: Flights and Hotel booking. Holiday Packages: Good discounts within India or foreign holidays. Weekend breaks: Many options for your weekend holiday destinations.