Apple places a high value on their own OS X software and their own design chops. Most people, even those who hate Apple, will confess that their chassis designs are often leaps and bounds better than most other PC makers. Just look at the Mac Pro versus any other PC workstation. The Mac design is in a league its own. Of course, whether or not it's worth paying a premium for a computer to look good is something that can only be determined by the consumer. Some people couldn't care less what the case looks like, as long as it's a powerful and reliable machine. But here's a fact: there's a price premium associated with Apple designs, and it varies from machine to machine. There's really no arguing that. Apple machines tend to, in general, cost somewhat more than PC counterparts with similar specifications, and design is one of the huge differentiating factors that's hard to put a solid value on, though obviously that value is definitely tangible.
Now, let's touch on software. Apple clearly feels that OS X is superior to Windows. They tout the operating system as being more stable than Windows (though that can argued) and less likely to be targeted by viruses. The latter has more to do with virus makers targeting the OS with the widest audience than anything else, but no matter the reasoning, there's no arguing that Macs get hit with fewer viruses and other assorted malware. Again, this comes down to a personal decision by the end users. OS X is not right for everyone. Neither is Windows 7. Most of the reason for the "Apple Tax" argument revolve around disagreements here; Mac users generally assume that the OS X operating system is worth paying extra for, while Windows loyalists cannot understand why anyone would pay extra while Win7 handles their needs just fine.
In the end, we found each Apple machine to cost more than a similarly equipped PC counterpart, with the baseline Mac Pro being the exception. Usually the delta is around $50 to $150, and even that can be mitigated by using an educational discount or otherwise finding a deal from one of the many Mac e-tailers out there. Furthermore, each new Mac comes with $99 off of a printer, and there actually is a $99 printer you can select; so, if you need a new printer, that's an imputed $99 total system savings.
We did want to touch on desktops quickly. Apple essentially has no consumer-level desktop outside of the iMac. For example, there's no "headless iMac" to select. The only tower desktop sold by Apple has a Xeon server-class processor in it; nowhere is the option to select a more mainstream Core i7 CPU. Thus, it's impossible to compare Apple's tower to any of the various gaming towers on the market. If you're a gamer, and you need a desktop, Apple shouldn't even enter the discussion. They simply aren't catering to that market much, if at all.
In conclusion, yes, most Apple machines cost a bit more than similar PC counterparts. But if you put a great deal of value on longer battery life, generally improved resistance to viruses, eye-catching designs that use high-quality materials, and will make use of the robust iLife '11 software suite, then the tax--if you can even call it that--is worth paying. The real take-away here is that there's no reason to argue whether or not the Apple Tax is worthwhile; it will always be a case-by-case value-based decision for each consumer. Depending on your needs, one product or the other will or won't make sense. Now, can't we just all hug and make up?