From the Apple Store you are guaranteed to get the standard price on everything. You're likely to get newly introduced products faster from Apple than from another authorized dealer because Apple seems to fill their own pipeline first before shipping to dealers.
You won't have the flexibility of choosing non-Apple alternatives, say, third party RAM instead of Apple's overpriced RAM, other than the limited line of accessory items that Apple Store offers. You will pay the legal sales taxes for your jurisdiction; as opposed to ordering from out of state/province and "forgetting" to voluntarily declare the purchase to your local revenue people.
There are also reputable third party online sellers, their policies will vary, however they have the flexibility to bundle other non-Apple products with the Mac and possibly save you money. Check to verify that they are an Authorized Apople Reseller. You also may be able to save on taxes and shipping. You will NOT be able to make more than a couple of dollars savings under the Apple Store price on the Mac itself because Apple only gives the dealers a 3% - 7% wholesale discount from the retail price. On the other hand, dealers who stock Macs sometimes can offer a good price on last season's model when new Macs come out, as long as you don't mind being one step behind TBE.
Apple and a few others sell reconditioned Macs, which can be a savings if you don't want top of the line newest models. Read all of the fine print first.
There are also, unfortunately, some ripoff artists, individually on eBay and even some with good looking internet storefronts with phony authorization logos. See the sticky forum thread on fraudulent dealers. Investigate the seller thoroughly and get independent feedback on them before entering into a transaction. Only use a charge card, never Western Union, Certified Cheque or bank wire transfer. PayPal gives you limited protection only. Read the fine print. If you are being offered a "new" Mac for more than 10% below retail, turn and walk away. Chances are it's either used, stolen, missing parts, gray market and/or an outright fraud. Do not consider any new machine that will be shipped from overseas after you pay for it. The Romanian Powerbook / Western Union scam is legendary.
Amazon is a great place, especially if you dont qualify for an EDU or Dev discount. There isn't usually sales tax, they have a number of rebates available on apple systems, shipping is reasonable, and finally, if you use a9.com as your primary search engine for a few days, you will automatically qualify for a 1.67% discount.
Also, if you are not paying sales tax, you can always put that money towards a faster shipping option, getting it to you quickly and probably still at a cheaper price than from apple.
looks like i've been checking out about 20 different websites on 2 comptuers... regretably a PC being one of those, but that's why im getting the mini, the pc has already crashed twice since my last post (above)... and it looks like i will be supporting the "mothership". It must be because of the EDU discount. Thanks apple for making things easy... i apologize for looking elsewhere...
I prefer to purchase directly from Apple. Especially from my local Apple Store. To me having that personal relationship is very important. When the staff gets to know a person, chances are they will go the next mile to be helpful. This will directly help Apple. I also consider the ProCare Card to be important, it is only available if the Mac is purchased at the store or the online store while there.