The February 2010 issue of Science Watch has the list for the 10-year period 1999-2009.
Of greater relevance to India: an IIT makes it to the list at No. 11 with over 25,000 citations and over 7000 publications.
The list doesn't specify which IIT it is, but from the context, it appears to be IIT-K. [Correct me if this is wrong].
Update [9 February 2010]: All the five commenters (so far) have pointed out that it's probably the entire IIT system that is at No. 11 in that list. I think they are correct; Ram (in comment #2) is especially persuasive.
The reasoning goes like this: The average number of papers from the five original IITs is between 800 and 1000 per year now, and it was half this number as recently as 6 years ago. The Science Watch article says the analysis is only for 'engineering'; so, it doesn't count papers in 'science'. Heck, its definition of engineering is so narrow that it excludes quite a few engineering disciplines -- for example, my field, metallurgical and materials engineering, doesn't figure in the list. Nor does chemical engineering.
Given these facts, a total figure of 7000 papers in 'engineering' in 10 years makes sense only for the IIT system as a whole, and not for any single IIT.