A couple weeks ago I generated a list of the theoretical physics papers that were most heavily cited during 2006, according to the SLAC database, and discussed it here. Today the people at SLAC put out their own lists for 2006, which are quite interesting to go through. Their data is quite consistent with mine, although the numbers are very slightly larger, since a small number of new citations have been added into the database over the last couple weeks, I think mainly from papers which for example appeared on the arXiv in January 2007, but carried 2006 dates (e.g. write-ups from 2006 conferences).
The main list covering all HEP papers is dominated these days by astrophysics-related papers. Out of the 50 papers on the list I count only about 15 particle theory papers, and 3 review articles. The only post-1999 hep-th paper that makes the list is the KKLT landscape paper. To make the top 50, a paper needed to get 152 citations or more.
The list I put together goes deeper, down to papers with 100 citations, but SLAC has also put out something even better: 2006 lists of 50 most-heavily cited hep-th and hep-ph papers. To make the hep-th list, a paper had to have 62 or more citations. Looking over the 20 or so post-2000 papers on this list gives a good idea of what topics have been popular in recent years: the landscape, dark energy, and various aspects of AdS/CFT, and a small number of other topics. There are also several review papers on the list. Anyone interested in understanding what topics are attracting attention in particle theory research these days should find it quite interesting to go through this list, and spend some time taking a look at and learning about any of these papers that are unfamiliar.