Nicholas Markwell has kindly produced a summary of the findings which is reproduced here.

The long-awaited report into the 2003 geophysical survey of the eastern quadrants of the henge was finally published in 2012. The author of the report has correlated the positions with Isobel Smith's 1965 estimated numbering in a table, and I thought it might be useful to summarise this here.
Smith's estimate of 98 stones, which was based on average spacing in the eastern quadrants, is now known to be incorrect, as the irregular spacing found by Keiller in the western quadrants is also evident in the eastern. The revised estimate, based on the discovery of sarsen fragments indicating burning pits, and also from parch marks discovered in the RCHME surveys of 1990 and 1995, is now 100-103, with 102 considered to be the most likely.
Smith and Lukis' 1881 probings revealed 15 stones in the eastern quadrants of the Outer Circle, but missed a further 5. Retaining Isobel Smith's numbering for the sake of convenience, the stones now known to exist are as follows, with dates of discovery:
The north-eastern quadrant:
50 standing
58 buried (1881)
59 buried (1881)
67 buried (2003)
68 standing
69 buried (1881)
70 buried (1881)
71 buried (2003)
72 buried (1881)
73 fallen
The south-eastern quadrant:
77 fallen
78 fallen
79 buried (1881)
80 buried (1881)
81 buried (2003)
82 buried (2003)
83 buried (1881)
84 buried (1881)
85 buried (1881)
86 buried (2003)
87 buried (1881)
88 buried (1881)
89 buried (1881)
91 buried (1881)
92 buried (1881)
98 standing
1 standing
It might be interesting to summarise the numbers of stones presumed destroyed, standing, fallen, buried, and reconstructed (again, using Smith's 1965 scheme for convenience):
Outer Circle (52 surviving out of 98)
46 presumed destroyed (assuming that stones 2, 25-29*, and 74 are not still buried under buildings and roads)
26 standing (stones 1, 4-10, 12, 14, 16, 24, 30-36, 40, 42, 44, 46, 50, 68, 98)
20 buried (stones 58, 59, 67, 69-72, 79-89, 91, 92)
3 fallen (stones 73, 77, 78)
3 stumps (stones 22, 38, 41)
* Stones 25-29 may still be buried and found by future geophysical survey, according to Martin Papworth: "In the western part of the henge, Keiller did not excavate stone positions in gardens either side of the High Street (25) - (29), where Stukeley shows a standing stone and two fallen stones no longer visible."
Southern Circle (5 surviving out of 29)
5 standing (stones 101-103, 105, 106)
The "Z" feature, Obelisk, and Stone D (6 surviving out of 14)
6 standing (stones iii-viii)
Northern Circle (6 surviving out of 27)
3 standing (stones 201, 206, 209*)
2 fallen (stones 207, 210)
1 buried (stone 225, discovered in 1881)
* Stone 209 is now standing on the northern verge of Green Street. Smith has this to say: "It had been built into the chimney-corner of a cottage and was left standing when the cottage was pulled down in order that it might eventually be returned to its original position in the circle." Having recently seen this stone, it is around 10 or so feet south of its original position.
Inner Northern Circle (2 surviving out of 12)
2 buried (stone E, parts of which are still visible*, and stone G, discovered in 1881)
* According to Smith, this stone may in fact be three small stones: "Small parts protrude slightly above the surface of the ground. It has been dug round by Smith and Cunnington and subsequently by Gray, who states that he found three stones covering a length of 16.5 ft. and buried in the solid chalk. These he believed to be parts of a single large stone. From his description, however, it seems rather more probable that there are three small individual stones, buried in a communal pit, as were stones v-vii in the Southern Inner Circle."
The Cove (2 surviving out of 3*)
2 standing (stones I and II)
* There may have been 4 stones. Plans by John Aubrey (1663) and Walter Charleton (1669) show a fourth stone, which Charleton describes as "a Triangular stone, of vast magnitude, lying flat on the ground; but, (probably) at first imposed on the heads of the other three, in the manner of an Architrave."
The Ring-stone
1 stump
Stukeley also records a stone several feet east of stones 33 and 34, and thought at one time that this indicated that the outer circle was originally a double ring. To test this, Keiller excavated, but found nothing. However, Stukeley had over-estimated the size of the outer circle, and thus the position Keiller excavated (marked on Isobel Smith's plan as "cutting I")was very likely incorrect. If this stone did indeed exist in Stukeley's time it's likely it was subsequently destroyed.
In summary, there may be up to 112 stones destroyed. There are 42 stones standing, 4 stumps, 5 fallen, and 23 still buried, giving a total of 74 stones within the henge today. Of these, there are no fewer than 29 stones (23 buried, 5 fallen, and 1 [stone 209] moved out of its original position) awaiting restoration to their rightful places within the circles.
It's interesting to compare these figures with the situation in 1936, when just 27 stones were visible:
15 standing (stones 1, 8, 32, 33, 44, 46, 50, 68, 98, 101, 103, 201, 206, I, II)
9 fallen (stones 14, 73, 77, 78, 102, 105, 106, 207, 210)
3 partially buried (stones 7, 12, E)
36 fully buried (stones 4-6, 9, 10, 16, 30, 31, 58, 59, 67, 69-72, 79-89, 91, 92, 225, iii-viii, G)
Keiller was responsible for re-erecting 26 stones, 15 of which were partially or fully buried (stones 4-7, 9, 10, 12, 16, 30, 31, iii-viii, excluding the stumps of stone 22 and the Ring-stone), 4 were fallen (stones 14, 102, 105, 106), and 7 were recovered from walls and buildings (stones 24, 34-36, 40, 42, 209, excluding the stumps of stones 38 and 41).
Nicholas Markwell

The original report by Martin Papworth was published in "The Wiltshire Archaeological & Natural History Magazine" Volume 105. 2012.

Further sources:
"Guide to the British and Roman Antiquities of the North Wiltshire Downs in a Hundred Square Miles Round Abury" by the Rev. A. C. Smith (The Marlborough Natural History Society) 1884, pp.137-145
"Avebury Summary of Excavations, 1937 and 1938" (The Morven Institute of Archaeological Research), reprinted from Antiquity, June 1939, pp.1-11
"Windmill Hill and Avebury, Excavations by Alexander Keiller 1925-1939" by I. F. Smith (Oxford University Press) 1965, pp.175-205, and the Addendum p.223
"Avebury Reconsidered from the 1660s to the 1990s" by Peter J. Ucko, Michael Hunter, Alan J. Clark, and Andrew David (Unwin Hyman) 1991
"Landscape of the Megaliths, Excavation and Fieldwork on the Avebury Monuments, 1997-2003" by Mark Gillings, Joshua Pollard, David Wheatley, and Rick Peterson (Oxbow Books) 2008