Can you give us some technical information on how you handle coordinate systems and transformations?
We process and store point clouds in ECEF geocentric coordinates (Earth-centred, Earth-fixed. See this Wikipedia article). Storing everything in a common coordinate system allows us to merge data from different reference systems when required. All of our spatial indexing is done in this coordinate space.
To perform coordinate conversions, we use the proj.4 library. This is commonly used by many geospatial applications. Its been around since 1995, and is very well regarded.
Our spatial reference system list is the standard PostGIS coordinate system list. It contains most of the EPSG codes that are in common usage. If you need to find the proj4 strings for other coordinate systems, some good websites are:
For height datum conversions (ellipsoid vs geoid), we use the standard EGM2008 5ft grid file to ascertain the geoid-ellipsoid height separation.