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Good questions Troy
You're right, most CCD cameras will out FITS in 16bit unsigned format.
The 16bit space doesn't last long either as most image processing software will manipulate it to a higher bit space depending on functions utilised. A simple example of this would be using a sum combine function where the value of each pixel in each sub is an addition to the final pixel value. Clearly if the software left the data in a 16bit format it would easily clip values over 65k, hence the software automatically increases the space giving the user two options when it comes to saving the image, either save at a higher bit space such as 32bit or IEEE floating point format or scale the data down back into the 16bit space.
I personally don't sum data often, but even with other functions such as median combine its possible to have masters higher than the 16bit 65k limit. For this reason, if working with FITS along I typically leave the data in IEEE floating point format.
The challenge of course is interoperability between other software processing tools. FITSLiberator will allow 32bit FITS to be loaded into Photoshop, but many of the advanced functions can't be applied in 32bit mode, thus the file needs to be converted to 16bit. There are a variety of ways to scale data down, most tools automatically scale, where others you'll get better results manually performing the task with pixel math or log stretching. Depends on how much control you want over the data.
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