One of the things that I think helps HRW (and something that some who work there express pride in) is that they are not dependent on public donations to the extent Amnesty is. HRW gains most of its donations from fewer but far more generous philanthropists. They would argue that this allows them to play less of an advocacy role than Amnesty has to and focus more on balanced scholarly work that attempts to "inform" the public debate, rather than push it.

Leave None to Tell the Story is a great piece of research by Allison De Forges, its up there with Linda Melvern's and Gerald Prunier works on the Rwandan Genocide. I think though the best recent work (at least to get an issue on the public's radar) was on the 2005 Andijan Massacre piece Bullets Were Falling Like Rain.
http://hrw.org/reports/2005/uzbekistan0605/