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 Originally Posted by Jack Sawyer
Well, according to computing lore the place where you need to spend the most money is in the case, power supply and then motherboard.
I've never heard of spending the most money on the case - I know plenty of people who have a fairly average case but a great setup inside. If you're building a server setup with hot-swappable drives you're in very difficult circles to me though! 
If you want to play games, your key components will be your:
Power supply
Motherboard
Processor
Memory
Graphics card
With your budget, you can get very good quality products in every area. If you had less money, I'd advise buying a cheaper processor or less memory as these are upgradable in the future but I think you've got enough money to go for everything at least medium if not high end straight away.
I'd avoid Thunderbolt for now for the reason JackSawyer said - there's an early adopter tax. Also remember that seeing as 99.9% of people don't have Thunderbolt compatible PCs, they'll have to have adapters/add-in cards/etc to make sure that everyone can use it, or they'll have USB as well as Thunderbolt on the device.
I think a single 2TB 7.2k RPM drive will be more than fast enough with the SSD for vital/commonly used software. Having your storage drives in RAID0 makes no sense to me as it doubles the chance of failure while giving a kinda unnecessary boost in speed. RAID0+1 makes your drives redundant but costs you a full drive in space. I don't think you'll necessarily need 240GB of space on the SSD either - you'll only be keeping key stuff on there so decide yourself whether the saving is worth it.
For the motherboard, I'd pick a quality brand on a platform you like but it doesn't necessarily have to be expensive. Tons of motherboards these days have ridiculously unnecessary features like LED lighting systems and millions of ports you'll never use. There's a lot of trusted brands out there - Asus, AsRock (Asus' budget brand), MSI, Gigabyte for example.
Just my 2 cents - I think I come from a different PC background to JackSawyer which would explain our different answers
EDIT: Just to expand a bit of RAID0 and add an analogy. Basically, imagine you have a warehouse with one employee. An order comes in and your supervisor tells you what you need - 20 boxes from all across the warehouse. You go and get the 20 boxes and give them to him. That's a single hard drive. Now imagine that there's 2 of you and the supervisor tells you he needs 10 boxes from each of you - obviously it's ~twice as fast, limited by how fast the supervisor can tell each of you what he needs. That's RAID0.
On the other hand, RAID1 involves writing the same thing twice to two different disks - a master and a slave copy. That way, if one hard drive dies, the other just takes over with no problems until you replace the dead hard drive and it copies all the stuff over again. You lose a bit of performance but gain instant backups.
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