Both types of games have their advantages. The flash games can be more fast paced and action filled while the php games tend to be text based and more in depth.
For puzzle games i prefer the flash variant since you get more of a gaming experience. The php games are more suited to mystery games and such.
But thats just generealzation and my humble opinions. Aocourese there are shining wxamples of stunnignly actionfilled php games and in depth flash games.
