Agatti (Lakshadweep) -- AGX (IA Dornier, which may be upgraded to ATR. Vijay Mallya wants an A319 grade runway)
Agra -- AGR
Akola -- AKD
Aizawl -- AJL
Along -- IXV 
Allahabad -- IXD
Bhatinda -- BUP 
Bareli -- BEK
Balurghat Airport -- RGH
Belgaum -- IXG
Bellary -- BEP
Bilaspur -- PAB
Bikaner -- BKB 
Car Nicobar -- CBD     (IA operates 737s seasonally)
Cuddapah -- CDP
Cooch Behar -- COH    (Alliance Air/Air Deccan)
Daman -- NMB
Daparizo -- DAE 
Dehra Dun -- DED
Deparizo -- DEP
Dhanbad -- DBD
Dharamsala -- DHM
Dibrugarh -- DIB
Dimapur -- DMU
Gaya -- GAY    (Sri Lankan operates Colombo-Gaya with an A320 seasonally and Thai Airways International plans a service soon as Bangkok-Gaya.) 
Gorakhpur -- GOP 
Guna -- GUX  
Gwalior -- GWL
Hissar -- HSS 
Jabalpur --JLR
Jagdalpur -- JGB
Jaisalmer -- JSA
Jamnagar -- JGA
Jamshedpur -- IXW
Jeypore -- PYB
Kailashahar -- IXH
Kamalpur -- IXQ
Kandla -- IXY
Keshod -- IXK
Kolhapur -- KLH
Kota -- KTU
Khowai -- IXN
Kullu (Bhuntar) -- KUU
Lilabari -- IXI
Ludhiana -- LUH
Malda -- LDA
Mohanbari -- MOH
Muzaffarnagar -- MZA  
Muzaffarpur -- MZU 
Nanded -- NDC
Nasik Road --ISK
Neyveli -- NVY
Osmanabad -- OMN
Pant Nagar -- PGH
Patina -- PAT
Pasighat --IXT
Puttaparthi/Sri Satya Sai Prashanthi Nilayam -- PUT        (IA operates an A320 Mumbai-Puttaparthy-Chennai seasonally.)
Raipur -- RPR
Rajahmundry -- RJA
Rajouri -- RJI
Ramagundam -- RMD
Ranchi -- IXR 
Ratnagiri -- RTC
Rewa -- REW
Rourkela -- RRK
Rupsi -- RUP
Satna -- TNI
Silchar -- IXS
Simla -- SLV
Sholapur -- SSE
Srinagar -- SXR
Surat -- STV
Tezpur --TEZ
Tezu -- TEI
Tiruchirapally -- TRZ
Tirupati -- TIR
Tuticorin -- TCR 
Udaipur -- UDR
Vijayawada  --VGA
Vishakhapatnam  --VTZ 
Warangal -- WGC
Zero -- ZER

(All are online or will have operations shortly --- mainly by Air Deccan.)

***

Indian Airlines
Offline Stations
Bhavnagar -- BHU
Bhilai
Darjeeling -- DAI
Hubli -- HBX
Mysore -- MYQ
Rajkot -- RAJ                           

(Air Deccan is planning Mysore, as Mysore is to have a planned runway upgrade for A320 operations, and Hubli.)

Indian Airlines
Online
Shillong --SHL
Jorhat --JRH
Gaya --GAY
Agartala --IXA

Air Deccan to start operations to
Vellore (Tamil Nadu)
Salem (Tamil Nadu) --SXV
Thanjavur (Tamil Nadu) -- TJV 

Pondicherry -- PNY --- Online for a week (Jagson operated a trial flight from Pondy to Chennai/Tirupati/Hyderabad with Dornier.) 

Thanks Nimish for starting this thread.

After seeing this list, am not surprised that Captain Gopinath is so upbeat!!! 
Also, almost all these were VAYUDOOT stations.