Water-cooling is a great way to have a cool yet silent system, and you'll probably appreciate the silence.
However, every few months you're going to have to change out the water, refill it etc. So it really depends if you're responsible enough to tend to your water-cooling system or i'll just not do it's job.
If you decide to go water-cooling, the best way is custom parts. Go with what Ownage said, DangerDen and Swiftech is probably the best for water-cooling.