Since you're going for a desktop machine, you may want to take a peak at this guide
I wrote for Kaff.
With that out of the way, let's dissect the Best Buy machine.
Processor
Crap.
Worse one possible to get. Remove the Q8200 chipset and spend about $100 more to upgrade to the Q9300 or Q9550. The Q9550 is "double" the speed of the Q9300 when it comes to processing intensive tasks like file servers, programming, etc. You won't notice a difference for FFXI but the Q9550 will have a longer shelf life than the Q9300 a few bucks more (~$10). If budget is more important than processing power, drop down to the Q6600 chipset for an extra $20. Even though this model is "lower" it'll still outperform the Q8200 chipset, in fact all the models I listed outperforms the Best Buy built Q8200 chipset. The Q6600 is 65NM instead of 45NM on lithography unlike the others but you not see the difference.
The reasoning is the L2 cache on the Q8200 is only 4MB. Ever since duo cores came out (well more like the high end single cores like the server class chipsets & xeon cores), 4MB L2 cache doesn't cut it no more. Have you ever brought a duo core computer and then wonder why its not much faster than your old computer? Its because there's a bottleneck in the processing that is slowing it down so you don't see the difference - unless you start memory intensive programs or heavy multitasking. Usually the biggest culprits are the L2 cache, RAM speed and front-side bus (FSB), in this case its the cache size, not FSB (the FSB is good on this one but more on RAM later on) . Better computers now have bigger L2 cache that goes above the 4MB to 12MB or they've added another cache level - called L3 cache. The Q9300 has a 6MB L2 cache size while the Q9550 has a 12MB L2 cache size. The Dell refurbished system chosed to have an L3 cache size of 8MB which accomplishes the same thing - faster processing speed than the Q8200 chip in the Best Buy machine.
Memory
Best Buy is notorious for ripping off their customers in this department. Let's do a little basic math in seeing how much the system costs to build.
1. Chipset - $163 (based on Intel's suggested retail price).
2. Motherboard - $300 (estimated by specified stuff included on their website and known compatible motherboards with included chipset above).
3. Hard drive - 500GB drives are generally $80 to $100 while 1TB drives (1000GB) drives are $110 to $170. Since they included 640GB, they must've used multiple drives and chained them together with a RAID controller or left them as separate drives. Assuming they used the cheapest of all drives to total 640GB, I'll say they spent $120 bucks for the hard drive.
4. Tower case itself - $40 (looks like a decent case)
5. Power supply - $50 (assuming they used the cheapest lowest wattage needed)
6. Various SATA, IDE, connector pins, etc cables - $15
7. Video card - $20 (Couldn't find it on nVidia's site. Looks to be a discontinued product)
8. DVD writer - $50 bucks
I'll stop there because that's already $758. I've already assumed all the parts are the cheapest available on the market. Now let's adjust for their discounts for being a retailer. Assuming a 50% discount all those parts cost them $379. Don't forget Microsoft. In order to install Vista on those machines, Best Buy still has to pay a licensing fee to Microsoft which costs about $200 bucks per machine. My company licenses directly with Microsoft for our licensing and based on the prices they give us, that is the lowest you pay for enterprise licensing (10,000+ machines). There is another level which pays lower licensing fees but as far as I know only the following pays that: Dell, Toshiba, Hewlett Packard, Asus, Acer, etc (notice the trend - actual computer makers). Best Buy doesn't make their own computers/laptops - they pay the various manufacturers to build it for them and then say "Best Buy exclusive". Which is bull-crap because it can't be. Its "exclusive" because Best Buy tells the manufacturer those are the options they want in their machines to sell.
Either way, Best Buy does usually skimp on the RAM. Many unsuspecting consumers will see "Ooh, 8GB of RAM" but will not know how fast the RAM is. To get around the pricing, Best Buy will put in 8GB RAM @ 400MHz, 533MHz or 667MHz - which is slow as fuck. If they put actual matching RAM that runs parallel to the FSB, that'll cost them $350 to $800 depending on brand name and latency. Usually you put in matching RAM so the computer can go fast not slow.
Ah fuck, this is getting too long. If you want best bang-for-the-buck, this tower is not for you. The Dell computer, while refurbished, will outperform the Best Buy model. Best Buy makes too much profit on this machine, well all their machines. Best advice is go to a computer specialist shop and not a giant retailer like Best Buy, Futureshop, Office Depot, Walmart, etc. While computer shops will try to get you to buy more crap, accessories, etc their computers are exactly what they're supposed to be. You get what you pay for at Best Buy when it comes to computers - cheap crap for cheap prices. While I will bash Best Buy on their computer products, I buy a ton of DVDs, Blu Rays and other electronics from them.
You don't have to spend $4000+ on computers to get a nice one. Each price range has nice bargains for each budget if you're willing to do the homework on them.