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This is an area of open research, with several research groups working in slightly different directions. So, I am not sure there is a consensus on what is the best approach.
http://openslam.org is a nice resource the provides code for some 2D and 3D SLAM systems.
Also, if you are looking for papers you may want to look at the archives for the RGB-D Workshop at RSS. http://www.cs.washington.edu/ai/Mobile_Robotics/rgbd-workshop-2011/home.html
The biggest problems I see with large scale mapping is managing the massive amount of data coming from the sensor and limiting the growth of the map over time without discarding critical information. One solution is to simply wait for Moore's law to provide faster processors.
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