Well my system isnt "Silent" as Dell/Alienware advertised back in 2011 so I figured that it might be the cooling going or just maybe im pushing my system to much. I also read that its never good to use stock cooling, but I wasn't sure if they meant just fans, not thermal/liquid.
Depends what kind of heatsink the system has you could get away with just getting a new fan(s), or get a new heatsink and fan. You shouldn't really need water cooling if you don't go for extreme overclocking. Also try to check what fans are making the noise (cpu, gpu or chassis fans). For gpus replacement fans might be hard to find and for cpu it depends on the heatsink.