For specific usages (individual point processing and interaction with other geometries) I'm using Postgis <http://postgis.refractions.net/>. However, I don't know of any way to directly load .las files.(GPL)
R (http://www.r-project.org/) is also a nice tool for particular processing however it doesn't hold lots of points at the same time and it's slower than C++ but you have access to a panoply of (statistical) tools. (copyleft) That said, it's a nice question and I'm happy to learn about new tools ! Etienne
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