PAL, with 50Hz refresh, is the television standard used in Europe and in some other parts of the world. NTSC, with 60hz refresh rate, is mainly used in North America, Canada and Japan. You can determine the region of the M by lookng at the Rom Browser or starting a game a looking at the fps / VIs counter at the bottom right corner of the window.
The main difference between PAL and NTSC is that PAL games generally run 17% slower than their NTSC counterparts, thanks to this 10hz difference.
Anisotropic filtering is a technique used in computer graphics to make minute details that are far away from the camera appear sharper (basically it determines what kind of filtering is used on the visible textures). Anti-aliasing in turn is a technique to reduces the "jagginess" of computer graphics (aliasing). Both of these can be enabled/disabled and adjusted in PJ64 graphics plugin configuration window. Having these enabled can affect performance if your video can is older and your computer is relatively slow.