Jabo's Direct3D 8 is for people who have at least DirectX 8 and want to play most N64 games.
Jabo's Direct3D 6 is for people who play particular games that work better with this plugin, such as Winback Operations and Yoshi's Story, or who do not have at least DirectX 8 on their system.
Direct3D 6 is also more helpfully complex than Direct3D 8 in configuration, combiners, blenders, texture rendering, etc. in areas that Direct3D 8 does not allow configuration for. It also has chances of emulating games faster than Direct3D 8.
Basically, you can't quite say Jabo's Direct3D 8 is better than D3D6. There are several advantages arguing vice versa.