I know this thread is very very old, but in case anyone ends up here like I did, I have some insight. Full disclosure: I am an employee of Best Buy. My official title is "Apple Computer/Tablet Sales Consultant." Here's my .02 on the whole Apple Store/Best Buy debate. I purchased both Macbooks I have from Apple.com. I am very happy with them, because I have a very demanding computer use lifestyle, and there are certain options I must have. If you are the same as me, then your only solution is apple.com. If one of the pre-configured models on apple.com is right for you, then here's my advice:
Buy from Best Buy. Not because I am an employee, because I am a customer. Applecare is a great plan, and is an excellent value in terms of extended warranty and INCLUDED technical support. Best Buy's Geek Squad Protection and Tech Support are two separate services, and of course can be bought together, but for considerably more money. Also know that Applecare is available on a Mac you buy from Best Buy, if the 18 months same-as-cash is something you'd like. Jimmy Greystone was exactly right about the retroactive interest if you take longer than the 18 months, though.
Here's why I fully stand by the Geek Squad Protection I sell every day, however. Applecare is considerably cheaper, but it covers no kind of accidental damage, unless it's on an iPhone. All it is is an extended warranty, just like for a car. They will fix all the stuff that breaks, but if you wreck the car, you are still out of luck. The GSP is like an extended warranty and insurance in one. There are several added benefits to GSP also, such as no-lemon and no-wait. If your computer has to be fixed three times for any reason, boom, new computer. If your computer can be fixed, but parts are on backorder for more than 14 days, new computer. While the GSP IS a repair warranty, if your computer can't be repaired, you get a new one. Not a rapid replace refurb model, a new one off the shelf. If the computer you bought is no longer available, you will get a new computer of equal price/specs off the shelf. That helps with the obsolete computer issue. It's also worth noting that the accidental damage coverage is not limited to a certain number of claims, and there is no deductible when you make a claim.
As for the Tech Support, it is just what it sounds like it would be, 24/7 support, phone, online, in-store, etc. It also includes services like virus removal, OS installs, software installs, and discounts on all other GS services not covered, such as house calls. The bonus to GSTS is that it covers 3 computers or tablets. So if you are replacing a PC that you have at home, get a Mac, and then later buy an iPad, all 3 of those devices are covered under the GSTS.
I know my opinion sounds terribly biased due to my employment by the company, but i love Apple computers, and I'm happy for anyone who gets one, regardless of where they buy. I just think that Best Buy's services, while pricier, are packed with value.