OK - looking at the base model Alienware machine (Area 51-7500), and pricing equivalent components at Newegg, I could build a machine for which Alienware charges $1899 for about $1420, including shipping and $80 of mail-in rebates. I will post the spec as soon as Newegg's server updates my list to be public. Let's call the difference $500, and consider how long it would take for you to build and tweak the system yourself, download drivers, etc. Figure maybe 10 hours from arrival of boxes to functional, tweaked system, and if your time is worth $50/hour, you break even. I haven't gone back to see what a high-end system would come in at, but given that my system was about 25% lower in cost, you could probably build a $5000 Alienware box for about $4000. Time would be a bit greater, since you would likely be dealing with SLI configuration and a liquid cooler as well, but if you have the savvy and desire to build your own box on a budget, you can do so quite well.
What does this mean in terms of Alienware's profit margin? Hard to know precisely, but pretty large. They will get parts less expensively than we could (the costs I have are discount retail), but they have to pay for salaries, facilities, advertising, customer service, and such that a homebuilder doesn't worry about in general. Bottom line - Alienware provides a number of services aimed at helping the less than computer savvy customer who wants a high-end system he or she can be proud of, and they charge for that service. Alienware exists and is quite profitable because there is market demand for the services it provides. They do all of us as gamers an indirect favor by increasing the number of top quality gaming rigs in use, which in turn helps justify the development of faster and more powerful games, graphics tools like DirectX, and ever more amazing graphics cards.
As far as the original question goes, I am pretty happy with my thesis that so long as neither Dell nor HP meddles with their new acquisitions, we as gamers will benefit from better, more affordable systems than ever before.