I tried to make a list of options avaliable
1) indiflight A nice tool which allows you to find cheepest flight to multiple destinations, on multipe days and using break journeys.
2) makemytrip Huge publicity, but it charges extra for credit card bookings.
3) rediff good plotting tools, fast site.
4) flightraja fast flight, with a persoanl touch. The agents actually call you to confirm the bookings
Then to book international travel tickets:
Stic travels is specially useful. They get the best discounts, yet ensure hassle free luxurious travel.
Bus tickets use redbus. It has a very fast query engine. However its services are limited to Chennai / Bangalore originating routes and does not support KSRTC/government operators.
For train travel, I guess one has not much choice but to go for irctc. Even though it is the only govt body in my list, the service is good. Tickets get delivered in time. However the user interface needs lots of upgradation.