Alblaka, may I ask how come the induction furnace exists in "stock" IC2 but the other machines don't have versions at the same tier? Is it simply because you think the furnace is the machine most likely to be used more than the others, or what? Just wondering, really
I'd say that in your situation installing Linux from the beginning isn't a bad idea. Ubuntu is a good starting point if you haven't used Linux before and it will run very quickly on your PC as well.
In terms of Minecraft/IC2, it will probably be a little harder to get them up and running compared to Windows, but it's certainly not impossible. I wouldn't consider trying to run games like Skyrim in Linux under WINE - it's going to be way more hassle than it's worth from what I hear. I might be wrong though.
Anyway, you can always buy Windows later on if you decide that you want to switch to it, and have the money available.
Everything looks fine there to me, really. A few things though:
I'm assuming you're overclocking, since you picked the 2500K over the 2500. You're not going to get an amazing overclock with the stock cooler so I'd recommend getting a cheap aftermarket cooler like the 212+ or 212 Evo. The Evo's slightly better but it's a really small difference so I'd just grab whichever one's cheaper.
It's probably worth springing for 8GB of RAM straight away if you can fit it in your budget. Using a single 4GB stick is going to be slower because you need 2+ sticks to run in dual channel mode. Also, depending on what other stuff you have going on, running a Minecraft server plus the client might take you over 4GB. Testing just now, I'm at 3.92GB of usage with my regular background tasks (web browser, email, etc.) plus a Bukkit server and the Minecraft client with only myself logged in. If I'm running a more intensive situation before I start playing Minecraft, and I've got a couple of people playing with me, I'm usually looking at around 5-7GB. Just something to bear in mind.
For the power supply 500W will be more than sufficient. Something like a Corsair CX500 will do well, especially as Newegg currently have a deal to get 15% off.
If you are considering running a server separately, you don't actually need a very fast computer for 1-2 people. At one point I ran an IC2 server with 2 people on my old laptop - 2.13GHz single core Pentium M, 2GB of DDR2 and a 5400rpm IDE drive. Didn't really encounter any issues with that but it was just easier to run it on my PC (similar-ish to your proposed one - 2500K @ 4.5GHz, 8GB, GTX 460)
If you're after a 320GB drive, the Samsung Spinpoint F4 is the fastest one out there right now because it uses a single platter, which is pretty awesome. Oh, don't get drawn in by drives that use SATA 6Gb/s (also incorrectly referred to as "SATA III") because no regular mechanical drive is going to come anywhere close to the maximum bandwidth of SATA 3Gb/s, so they're basically just making you pay more for something that won't make any difference.
As for the motherboard, I'd go with the Z68 chipset like you have, but you can pretty much just pick any board that you like the price and features (number of SATA ports or whatever) of. The motherboard with Sandy Bridge doesn't affect the overclocking performance nearly as much, and I'm assuming you don't want to go for a huge overclock anyway, so you don't really need to worry about that. I've got a Z68XP-UD3P which is a fairly nice board, but it's probably out of your price range.
I haven't read through all of the posts, but regarding the graphics card:
From Nvidia, the 460 and 560 are the same (with the 560 usually having faster clock speeds, something overclocking the 460 would solve) but the 560Ti is faster than both.
The 560Ti falls somewhere between the 6870 and 6950, probably closer to the 6950.
If you're considering buying an older generation card, bear in mind that the 5870 is faster than the 6870 and that the 5850 falls between the 6850 and 6870, confusingly.
Anyway, the 460/560 is a great performer and is what I'd recommend for an Nvidia card, if you want to go with AMD then a 6850 or 6870 is probably your best bet, depending on what price you can get one for.
EDIT: Wow, that ended up being a really long post xD
As for PSUs mounted in the bottom of the case, most people find them preferable, hence why almost all modern cases apart from the cheapest ones have moved them down to the bottom. You do have to ensure that the case has a decent ground clearance if you mount the PSU with the fan facing down, and obviously make sure that there's not a bunch of dust under the PC. That probably doesn't work too well on carpeted floors or rugs but it's great on my wooden floor. If you mount the PSU with the fan facing in towards the case, it won't disrupt airflow because in most PSUs it just won't run fast enough. What it will mean is that your PSU will help to exhaust some of the hot air from your case, the flipside being that the PSU itself will run slightly hotter due to the air it's taking in being warm rather than cool. So that could result in the fan speeding up and making more noise, but as long as you've got enough other airflow in your case you shouldn't find that a problem.
Talking of airflow, for a build like this all you need is to put a 120mm intake in the front or bottom and a 120mm exhaust at the back or on the top. Anything more is a bit excessive.
Looks pretty awesome, I'll definitely be following this.