1. I have a 200 watt crate 40 gc with clestion speakers and it makes a popping noise when my guitar plays low notes. It stops when i hit it on the top.
keep hitting it, get one of those birds that perpetually go up and down.

But seriously, could be a number of things, have a tech check it out if its too bad

you say '1' what other problems are there?
Sounds like a bad connection, probably in the preamp, since it's worse with higher gain. I'm not familiar with that model. Is it a tube amp?