Is that GTX 260 the best card for the money? Also, would it be in my best interest to get a DX11 card at this time? I most likely won't be overclocking unless the performance increases are noticable and substantial on any component. If I decide not to overclock, do I need a third party CPU cooler? I think I could probably save some money on the case, but I would like most of the features that the case I listed. Is this build the best system I can get for roughly 900-1000 dollars?
Case: You're spending way too much on that case. I highly recommend the HAF 922 or Antec 900.
Mobo: For $30 more (basically what you didn't spend on the case), you can get a USB 3/SATA III board.
RAM: For the same price, you can get the 1600 mhz CAS Latency 7 Ripjaws.
GPU: Definitely go with ATI. nVidia is being destroyed right now, and ATI's cards are much more future proof. I'd recommend the HD 5770 for $160ish. It's a little lower on the performance side, but it's cheaper, has DirectX 11 support, and is better in a dual card solution.
If you can squeeze the existing build by $90 through combos and what not, you should get an HD 5850 for $300.
PSU: OCZ StealthXStream 700W $60 after rebates. It's a good quality PSU for very cheap. It's also in a few combos...
DirectX 11 is not that useful today. However, the shift is inevitable. So it doesn't make sense to spend $200+ on a GPU today only to have to spend another $200+ later on to get DX 11.
Overclocking gives really good, cheap performance gains. Generally, it only takes the adjustment of a few settings. It's especially easy on GPUs, as both ATI and nVidia have a tool to do it, and no additional cooling is needed. ATI's 5xxx series is especially good for overclocking because they don't use much power any way.
If you do not overclock the CPU, you don't need an aftermarket cooler.
I haven't bought any open box items. I do know that you're likely to only get the actual part (no cables, no software, no screws, etc.). As far as quality, I believe the open-box items are just new items that have been opened to essentially scavenge for the accessories, but I could be wrong.
The cutting costs was mainly for combos, cheaper similar parts, and other deals.