I'm not brave enough to go with a water-cooled system, as it's pricey, but.. I don't find it necessary unless you really want to overclock or go with a quieter system.
I'm no pro, but I love building machines. Unless someone else is putting the system together, I would avoid the water-cooled system for now. Save the expenses from water cooling toward a better graphics card like you had mentioned. If you're going to be playing the latest and greatest games out, then that money is better spent toward the video card. If you'll be using it for basic browsing, email, etc... meh. That's like saying you have a Ferarri used as a grocery-getter.
I have my PC setup with a 64 GB SSD drive for Windows, another 64 GB SSD for Mac OSX, but the largest drive is a 1.5 TB drive partitioned into two to save the main programs. I don't care about immense speed, but I just like the much faster startup times. (I got the SSDs last year when the prices were about $1 per gigabyte, but now with Black Friday, rebates and more the price on SSDs seems to be around 50 cents per GB).
Black Friday's one of the best times to score deals. Cyber Monday is coming up, so keep your eyes peeled.