It's almost two years later but if you are using an Nvidia gpu then to solve this you need to go to nvidia control panel, 3D configuration and then turn on the triple bufer from there, it only affects opengl games and emulators and it helps to avoid that sugar honey ice tea lag
While we appreciate the helpful information, in the future, please try not to bump threads older than 6 months. One reason is that sometimes the advice for a given problem may be outdated (e.g. in this case, the OP and anyone else reading this might get rid of slowdowns by upgrading to the latest development revision of Dolphin and using ubershaders on Hybrid or even the immediate mode).