The Antec 900 was an amazing case... 5 years ago. I still have it as my main computer case, and it works, but the wire management is horrible.
This. For the most part cases are personal preference on looks, however there are some things you want to look for to get more modern cases. Air flow, cable management, and tool-less. I know all Lian-Li cases are tool-less and are fantastic. Right, Phobus?:lol:
Also, if you're on a $1000 budget the $50+ you could save getting a cheaper case can bump you up a tier in GPU or CPU. I would not get the Phantom or HAF 932 simply because of that. Unless of course you really care that much about spending money on a case.
Now for the actual build. Very basic parts for a gaming PC:
1. Motherboard
2. Matching CPU
3. Compatible RAM
4. PSU (wait for Reflex to tell you what's good)
5. GPU
6. Hard drive
When you pick a CPU for your budget (which most likely will be an i5 or comparable AMD) you want to check the socket for your specific chip. If you get an i5 2500k, look at the details and it says socket LGA 1155. Then when you search newegg for a motherboard, only look for LGA 1155. Anything else won't work.
Details on motherboards are mostly about overclocking potential. If you're interested in that you'll want to talk to some of the people who know more about that. Just look for USB 3.0 and SATA 6 for future-proofing. And of course if you need some demonic amount of USB ports, that might influence your decision.
RAM has clock speeds on it just like everything else. The important thing is that the clock speed for the specific RAM you buy must be at least equal to your motherboard's minimum. Anything higher will still work. Oh, and stay away from OCZ RAM.
For power supply, there's a specific list of what brands are good, and even which lines within brands are worthwhile. Reflex knows more about this than me, and will probably give you a full list if you ask. All I know is the Seasonic X line is in the "excellent" category, and that's good enough for me. Either the Seasonic X650W or X750W, depending on if you want to SLI/xfire down the road. More than that is just silly.
You say you don't want nVidia, but really once you get into higher tier performance that's your only option right now. For a $1000 computer, you'll probably be looking at GTX 460/70 or Radeon 6850/70. Somewhere around abouts there. Just keep in mind, nVidia actually improves with drivers so their cards will end up better down the road.
As for the HDD, just get a spinpoint F3 1TB. It's basically at the peak of price/performance. Going cheaper won't save you that much money compared to the amount of space you're losing. If you're interested in blowing major cash to speed up boot times, look into some SSDs. They're horrendously expensive and probably won't fit in your final budget, but by all accounts they're worth it.
I know Phobus has a build thread. If he's still doing that it's worth your while to answer the questions he's got in it.