I won't be any help re: water cooling, even with good closed loop coolers available it makes me nervous. Probably why my main rig runs in a Cooler Master HAF 932 and sounds like a jet engine, but I play games with my headset on anyway
For best CPU or GPU at a certain price level, I find Tom's hardware usually has some pretty good recommendations. I agree with their current suggestions
around the $200 price point: the GTX 650 Ti Boost 2GB or the GTX 660. Something to be aware of about their recommendations is they don't generally take power consumption into account, just price and performance. Also, if you end up with a case other than the Prodigy, you'd have to worry about physical size of the card as well.
On another note, my June 2013 Maximum PC just arrived in the mail, and I'll be damned if the cover story isn't a trio of $750 PC builds duking it out. They chose to represent the 3 most affordable major CPU sockets available right now (i.e. no Haswell since it isn't out yet) - FM2, AM3+, and LGA 1155. If you subscribe to the mag, or you can find a copy on the newsstand, I think it was interesting reading through what the guys each picked and chose to focus on. They didn't go Mini-ITX, but that really just means different choice of Mobo+case+PSU, and also means AM3+ isn't really on the table, since the AMD Mini-ITX boards seem to be all FM1 and FM2, as I believe LatiosXT pointed out earlier in the thread.