As Halcyon said, depends on your intent.
My computer building experience is this. When I was younger my intent was making the best gaming system that can run Crysis. I sunk alot into GPUs. Nowadays my intent is to run programs like J Model test which really need a system to be good at crunching numbers. So nowadays I sink my money into the CPU and RAM. For quick boots and start ups I like SSDs. You only need the OS and some programs installed on the SSD. Everything else like files pertaining to results, text, documents, movies, pictures etc can be on HDDs. As for PSU you need to calculate how much power you need from the specs of each part. Lastly I know we're moving to an age of downloadable content but I suggest planning for some form of CD/DVD drive and even a floppy. You may want to image/save a disk's content one day. Water cooling and overclocking is for pros and I wouldn't recommend unless you do know what you're doing (what to and how to set clock speeds and voltage levels in the bios for example). Regular air fans will suffice. You can even get the quiet performance water cooling offers if you pick the right fan (# of fan blades, rotational speed, rubber mounts, etc.)