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My chipset fan had a problem when I first got the motherboard where it would sometimes hit the fan gaurd and making a buzzing noise. I took it off and it quit but the fan did later but that wasn't the gaurds fault. See if it's running up against anything. If you want, you can get some nice quiet fans for cheap. There are many many fans that are made just for noise reduction.
Watercooling can be expensive and require some case modification (if you need a place for your radiator and it's fans) but it keeps everything pretty cool. If you are going to overclock I suggest you go with watercooling but if you don't really know what you're doing it may just be better to get some high power fans and overclock with those.
In conclusion: if you're looking to save money and get some new fans, do that. It's the cheaper of the two and you can still get some great cooling with fans. If you're looking to do some serious overclocking then go with watercooling. You can get starter kits or prebuilt ones that will just sit on your computer (you will still need to buy the chipsets) and they can cause some problems if you don't know what you're doing. Remember, water + electronics don't go good together will they aren't controlled, so if there's a leak, you could be screwed. That never happens with fans though so keep that in mind.
If you need some good sites, I have a few where you could look.
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