As one of the biggest AMD fanboys here, I will tell you that:
You should stick with Intel. The numbers you are looking for first is manufacturing technology. The best processors at the moment are made with 45nm technology (as opposed to 65nm) and as the numbers get smaller, it means the processors are doing more and better things with less space, heat, and power. AMD is due to release their 45nm processors in two months while Intel has had theirs out for nearly a year. Manufacturing technology is not always a numbers game, for instance AMD has some better processors out there than Intel's 45nm ones in terms of certain things but overall Intel's processors are better at doing their jobs.
The second number you are looking at is Front Side Bus speed or FSB. AMD uses a different kind of rating, but since you are going with Intel, you will be looking for 1333 MHz. Think of this as a processor's ability to communicate with the other parts of your computer. Make sure that your motherboard is rated at least for 1333 MHz. Any place that sells motherboards will display this number. The common motherboards are either 1066/1333 or 1333/1600; either will work for you. If you are willing to spend the money, find a board that also functions with DDR3 RAM, as opposed to DDR2, which is the standard. This will allow you to run much better memory in your computer, but will also cost you a noticeable amount of money.
Here is a list of the currently available 45nm Core 2 Duos sorted by price for your reference. They are identical except for raw speed, which is what you will be selecting based on. The higher the GHz, the better, obviously. The middle of the road E8400 tends to be the most popular.
Anyway, the Core 2 Duo Wolfdale series (those displayed in the Newegg link) tend to outperform all the processors on the market except well-made applications that support multi-core technology, in which case they are outperformed by the AMD quad-cores (but not the tri-cores) and the Intel quad cores -- but only barely. Otherwise the only processors that consistently outperform them are the 1000+ USD Core 2 Extremes.
As far as the graphics cards go, the 8 series tends to be better than the 9 series as due to a market trend, nVidia failed to deliver and significant improvements in their new cards. If you are going to purchase a 9 series, the new ASUS 9800 is the way to go.
This review here will tell you all you need to know about it and the conclusion page covers pricing points.
Lastly, your motherboard is a pretty big issue and you should make sure you pick a good one. You are looking for a socket 775, which is what the new desktop Intels use. Also, as mentioned before, you need a 1333 MHz FSB rated motherboard. If you want to shell out the extra dough, DDR3 capable boards will sport you a significant boost in high performance applications, but not so much in normal use and it will cost you a sizable amount more. Just remember that the DDR2 standard is starting to fade and that clearly things are all progressing towards DDR3.
Another important thing to consider is the name brand of your motherboard. This directly translates to not only what features it has, how well it functions, and the update cycle behind it, but also flat-out how well it will hold up. I have had the most experience with Foxconn, which makes most of the Dell motherboards and they hold up like champions. My newest computers have ASUS in them, which provides the most functionality and best updates as well as a swell tech support. Intel branded motherboards obviously go very well with Intel processors. Intel likes to say their own motherboards increase the performance of their processors -- whether you buy into that or not is up to you. I found MSI motherboards I have used tend to be very economical but not very good quality, though others claim to have good experience with them. Gigabyte and EVGA are also well-known manufacturers, but I stay away from anything that has nVidia chipsets (the controllers on the motherboard such as for the memory and PCI slots that communicates with the processor to run your computer) because I have had a number of very bad experiences with them and because several times nVidia has had to recall large shipments due to their own negligence, something I can't say about AMD and Intel, so I would advise choosing an Intel chipset (also called a north bridge).
Here is a decent sized cross-section of motherboards with the above mentioned capabilities for your reference, sorted by most reviews and highest ratings.