As tgunner wrote, there is a huge number of options allowed by a $1000. budget, so you'd have to narrow the focus for us to come up with a more targeted answer. Like what do you plan to run on this system. Is it storage intensive, Is it video intensive. Are you partial to either AMD or Intel, etc... It would be difficult NOT to come up with an excellent sytem anymore.
. Check the reviews over on the tech side of this site and other good sites. I'd say basic specs would consist of a dual-core processor, a mobo to match (I like to stick with ATX as there are more slots available and one never knows), 4 GB RAM (no more unless you are going to run a 64-bit OS - as anything above 3 is wasted on a 32-bit version of Win), around 500GB of hard drive space divided between two drives unless you are really running storage intensive apps like video editing as I like to keep a fresh image of the OS partition on a separate drive for quick recovery from problems, a couple of burners and that's about it. I like to keep a combo floppy drive/flash card reader in the floppy bay - you may never need to use the floppy for anything, but when you do need to, nothing else will do.
. For case and PSU, I'd recommend one of the Rosewill 5600 series like the R5605 which continues to demonstrate that you don't need to spend a lot for an excellent case. The new Antec Earthwatts EA-650 (made by Seasonic) is an excellent deal at $79.00 shipped (right now at the Egg) no matter what system you finally end up with, or what case. I don't normally recommend that large of a PSU, but since it is 80 Plus rated, you won't be wasting much energy regardless of the actual draw of your components and you shouldn't run out of safe margin on the high end either. Video card will depend on your specific needs so I won't recommend - plenty of good ones out there for under $100. I'm currently using the integrated video in my ASrock mATX mobo and it has been just fine for my purposes and the mobo cost less than $70.
.bh.