Ever since epsxe 2.0 was released the general recomendation runs like this
Pete's OGL2 core plugin (the one that comes with the emulator)-- is best for people who want more graphical enhancements and more a few of the graphical effects the the other core plugin does not do (this is less common an occurance).
The Core gpu plugin 2.0.0 is for people who don't want the graphical enhancements (except for the gte percision fix), or people who don't want to mess with settings as much to fix compatibility issues on a per game basis. It is also the perfered plugin on systems with less powerful GPU's or GPU's that have poor OpenGL support.
The various other graphical plugins (downloaded ones) have very specific benefits/use cases and are generally things you use if the other 2 options either do not work with your hardware or do not have the features/performance you want.