The number of publications from 2004 to 2008 has grown in all IITs and IISc. Here is the trend.
One can clearly see that IISc has the largest number of publications but the number of publications has increased significantly in other IITs. For example, the ratio of the number of publications in 2008 to the number of publications in 2004 is 1.2 for IISc, 1.7 for IIT-M and 2.0 for IIT-Roorkee.
I will post separately on the quality of publications but whatever parameters one takes: number of citations, number of citations per paper, h-index, number of papers in journals with impact factor of more than 5 etc., in each category, IISc leads the others. However, when one compares this output to that of the top 30 universities in USA, the output is still low. Therefore, this shows that there is a scope for lot of improvement for all institutions in India.