Preferrably all of them.
[HKEY_LOCAL_MACHINE\SOFTWARE\Volition\Freespace2] is used by all FS2 installations, including total conversions and mods. This won't be a problem to mods since they rely on FS2 and use -mod flag, but for total conversions it would be better to have their own registry entries.
For example:
[HKEY_LOCAL_MACHINE\SOFTWARE\Volition\Freespace2\TBP]
(Strangely it gets cut from middle of TBP...)
I am sure many would like to have seperate commandline options to both and at very least, -mod flag which is stored to registy will give trouble. In other words, TBP as well as other total conversions are supposed to be independent.