If you're concerned about CPU future proofing - what about the upcoming Core i7-3980X Extreme Edition with all EIGHT cores functioning! It's slated for the 2nd quarter of this year.
Cooling is a bit more interesting/confounding... I own the Noctua NH-D14 myself and have no problem with it, but there are a number of reviews and comparisons that give higher marks to the Phanteks PH-TC14PE. And the same thing goes for the Thermalright Silver Arrow SB-E. The Noctua is not cheap and you want to make sure you're getting the best. Do your own research and I'd like to hear what the others in this forum say about cooling because it isn't a frequent topic. Just be sure to keep the height of your intended memory chips in mind when selecting these heatsink fan units because (these three are) all of similar design - 2 fans & 2 radiator grids - and have minimal clearance over the memory slots.
1. Both the 3930K and the 3970X are unlocked, both are 6 cores, but the 3930K has only 12 MB L3 cache versus 15 MB L3 for the 3970X. That is about all the difference between the two, apart from the price, around € 500 versus € 940. Is that worth it? From my perspective, no. Both can easily run at 4.7 GHz overclocked and then the difference in L3 cache is negligent.
Jake mentioned the 3980X but I think he meant the 4990X, which is slated for Q3/4 and which may be an octo core. Time will tell. It is all rumors now.
2. Water cooling does not really perform better than air cooling. It only matters when overclocking severely and then the H80 is too small anyway. See Why not water cooling?
3. For PR 32 GB is enough, for AE it is wise to go for 64 GB.
4. Look for PCIe-3.0 8x controllers with 8+ ports internally (2 x SFF-8087) and the largest cache possible. Good brands to look at are LSI and Areca, with the 1882 series being a popular choice here.
5. If you missed anything, you can probably find it here: Planning & Building a NLE System