After installed compiz and enable 3D effect in my ubuntu,I found that it not running smoothly especially in moving windows around the screen.
Following settings make this smoother:
Open CompizConfig Setting Manager from System->Preferences->CompizConfig SettingManager.
Select to General->General Options->Display Settings tab.
Un-tick Detect Refresh Rate,set Refresh Rate to match the vertical refresh rate of your display.And tick Sync to VBlank.