The gelatinous stuff inside a squid–it might be clear, or it might be murky with half-digested squid prey–won’t hurt you. It’s technically edible, and the Japanese make a shiokara (salted, fermented marine animal viscera) out of squid innards. However, most chowhounds–and, apparently, even most Japanese–find it repulsive. kare_raisu describes squid shiokara as the “only thing I will not eat again,” though Ed Dibble finds it strongly flavored but tasty.
If for some reason you have a whole squid, and you’re not a Japanese shiokara master, you should probably just throw out the guts.
Squid- The insides of the squid