Bionicle: Matoran Adventures:
A game for the GBA. You play as both Matoran and Turaga during the Bohrok invasion. Nothing else I know of.
Battle for Mata Nui:
Somewhat a stragedy game. You take control of Matoran, Turaga, and Toa to fight the Bohrok. You can use items like Rust Bees to destroy Bohrok or let your units do the fighting. After that, you have the clean up the damage from the Bohrok.
The BIONICLE Guild
For BIONICLE fans (obviously)