Voodoo5 is better - there is no speed advantage, but V5 can do 3D acceleration in a window with 32bit desktop while V3 can't. This is because Voodoo3 has HW 3D support only with 16bit colors. Voodoo5 does work with current drivers in 3D mode.
V5 also support 15bit colors, which is useful with some older 3D accelarated games and demos.
-q