I look at the price of their drive options as opposed to my retail cost, the price of their very humble choice in graphics card (the Geforce 120GT 512MB is just a relabeled 9500 GT which puts it way behind the current state of the technology. . . surprising for a company that prides itself on it graphics capability.
You've got to remember that Apple, like HP, Dell, Lenovo, and other name brand makers, IS a retailer. They will generally sell their products at retail. They are not discounters (except for close-outs and refurbs). Apple well knows that you can get that 1TB hard drive from a discount house retailer who is basically selling his products to the public at wholesale prices. Often, manufacturers can get better OEM pricing from the component manufacturers IF they agree not to cut the manufacturers suggested retail pricing when selling the component separately. The component manufacturer has an interest in maintaining his product's price structure to its retailers.
The very real graphics capability of the Mac is less in the graphic cards than in OS X's Core Graphics. Apple, for example, was able to do amazing things in 2001 in its Aqua interface—even with older Macs with really limited graphics cards—that Windows Vista's Aero required a super graphics card to do in 2007.
You have to look at Apple's design and overall system philosophy for the reason behind the choice to not offer the latest and greatest components, except for CPUs. Apple wants to ship systems that "just work." They could very easily partner with a graphic card maker and always ship the latest and greatest graphic capability—but then there would be problems with newly developed capabilities, newly written drivers, and a compendium of issues unknown until the card has been in the wild for a period of time to shake out the gremlins. Apple long ago elected to install LAST YEAR'S latest and greatest, relying on their tried and true OS level graphic engines rather than the latest on-card solutions, so that they KNOW exactly how that card has reacted in the wild, that the drivers are solid, and the gremlins exterminated. That way, their customers can receive what Apple sells: computer integrated systems, with well tested components, engineered to work with the other components and software included in the system that Apple stands behinds and warrents; i.e., systems, for the most part, that "just work."
However, I stand corrected and am not afraid to admit that I am wrong and that the "Apple Tax" is way over stated in most cases when compared to other commercial PC's.
Good for you. For the Workstation class of computer, Apple offers one of the most economical and powerful models compared to the other name brands with similar capabilities, usually beating out the competitions' pricing by a long shot as in this example, where the Apple is $1,000 to $2,000 less than the equivalent model from HP. That HP Workstation, when it was originally introduced was over $4200 while Apple's—which was first to use the Nehalem Xeons, was just $2499.
Perhaps Apple's failing is that they insist on maintaining their price through the products' life (usually just quietly upgrading internals at the same price point) while PC maker's, competing against a slew of other makers using Windows, compete on price and lower theirs so that, at the end of the Apple computer's viable market life, before Apple refreshed the line with the latest and greatest, it WILL be more expensive than the PCs.
In almost all price point levels—except the low end where Apple has deliberately chosen not to compete, leaving that sector of the Mac line to the pre-owned (to borrow a phrase from the high-end used car market) Mac market, where one can buy a very reliable and still quite useable prior Mac model at reasonable prices—Apple's computers are easily competitive with the name brand competition in price and features that people want. Even in the mid-range all-in-ones, I could show you that the iMac competes very well against the name brand Windows PCs with similar grade and capability components.
It was right for the time. The PPC970 chips in those were screamers for the jobs they needed to do, way faster than any x86. But Apple was the only one selling them and hadn't come out with the rack mount systems yet, so they used the towers initially, with a plan for replacement when the rack mount systems came out.