Good question.

I often wrap metal zipper tabs in tape to quiet them, or take them off and replace with fabric or a ziptie.

Zippers can be lubed, I rub an old white candle on them.

Velco I do not know how to quiet, I try to avoid it. I prefer snaps on tactical pouches because it alerts the suspect less than the tearing sound of velcro does.

Clips, I guess you just keep them done up, you could even tape or glue closed the ones you do not use?

Mike