I think most popular is Koinex, because they have more cryptocurrencies. Also the prices to buy/sell are not different there as are in Zebpay and Unocoin.

I came to know a new exchange BITINDIA is coming up and they are going to have lots of coins. Currently they are asking people to vote which coins they want to people to get listed in their exchange in india.

Bitindia has John Mcafee as advisor/founder something like that.

If they turn out like they sound they will be huge.
 More over there is coindelta exchange which is also very good with number of different currencies. You can buy OMG and QTUM there. My current favorites.