The numerous pages of Denon IR documentation breaks down fairly easy. This is what I found looking at the 3808 codes:
They reorganized/reworked some of their Kaseikyo code sets giving the Main Zone, Zone 2, Zone 3, Tuner, Net Audio, iPod and XM their own unique device numbers. They also duplicated many of the traditional Sharp based codes with Kaseikyo code sets which indicates to me that they may eventually phase out the sharp codes at some point.
There is a ID feature which I do not fully understand at this point that allows for up to 4 remote ID settings to be set. I would imagine the the receiver can be set somehow to receive codes from only one of these sets.
Set 1 uses function codes 0-1023 for any given device number. Set 2 uses function codes 1024-2047 for any given device number. Set 3 uses function codes 2048-3071 for any given device number. Set 4 uses function codes 3072-4096 for any given device number.
Sets 2-4 seem to be very uniform in their construction in that specific codes use the same relative function numbers (sans the ID portion of the code) from set to set.
Set 1 seems all over the map because they used many of the Kaseikyo codes already in use by the '06-'07 line despite the more organized model they created for sets 2-4.
I have started to break down and document the codes and will have them available sometime soon for posting.
