HKLM\Software is used extensivly. That's where Classes is stored, as are all-user settings for everything. HKLM\System has tons of stuff in it. HKLM\hardware is used, too.

So I think HKLM is "really used". On NT4, there are the same 5 sybkeys. So if there's any real difference, it's between Win9x and NT/2000, nothing significant changed in 2k.