Plus:
You can signup for SMS alerts for lowest airfares and discounted holidays.
Travel tips, city guides and videos.

Minus:
Total air fair including taxes is shown on the last screen.
The airfare search does not include Air deccan’s flights.

Yatra.com offers holiday packages, flight/hotel booking (domestic and international), car and bus booking. I tried many combinations to find bus service; however, I could not find one. Yatra.com has a travel community portal Raahi, which has city guides, travel guides, reviews and more.

Plus:
Cash booking facility (in few cities) which no website provides
Let’s you find the best air fair +/- 2 days of your journey date.

Cleartrip.com lets you book domestic flights and hotels. The website has uncluttered design. Cleartrip has recently added city guides.

Plus:
You can find lowest air fare in a month through Cleartrip calendar
You can search air fares through mobile also, however, you can not book a ticket through mobile.

Minus:
Does not include Goair in flight search.
Show un-relevant flight options, while searching for flights between Mumbai and Delhi, results include Mumbai-Kolkata-Delhi flights.

Travelguru.com offers flight, hotel bookings, holiday packages and cruises (India and abroad). You can sign up for SMS updates from travelguru, however, unlike Make my trip you can not choose itinerary.

Ezeego1, promoted by Cox and Kings is a complete travel portal. It has flight, hotel, car, rail, cruise reservations, visa information, city guide and more. The rail reservation is for Europe only.

Apart from these travel portals there are few air fair search aggregator like Zoomtra, Mobissimo India, Yahoo India Farechase and Rediff Fair Search.

Out of these aggregators, Zoomtra has some good features like setting up the alerts for desired air fair and also shows the cheap air fair available in it’s ticker.