In my limited experience with road bikes I think this can apply across from MTB as well so I will give my advice. First I think it's important to explain why creaking is bad... If for anything it can be undue stress on the system, but additionally it is a loss in efficiency. Any sound at all represents a loss in the fluid transfer of energy.

Does this happen when you are riding normal or just when the handlebars are turned? I have seen this happen with caliper brake sets when the caliper is too tight. The creaking can come from the arms on bakes because they are too tight. Since it's common for brake routing to be pulled tight when the bars are turned to the extreme (this is not the best situation but it is common with some stock situations) the calipers are tightening when you turn the bars. This is my best guess assuming you have replaced the cables and housing. Obviously if both housing and cables weren't replaced then it could be a different story. If friction occurs in the lines causing clicking this could be the cause.