I was just running some numbers a few minutes ago. These are for the 13" base model, but they should give you an idea. Sales tax in my area is 8.5%, so you would need to adjust for your state.
If you want Applecare then you need to put that into the equation as well.
Apple Store: 1199+102 (sales tax) = 1301 Applecare 250 Total $1551
Apple Education Store: 1099+93 = 1192 Applecare 183 Total $1375
(If you buy online there's no need to prove you're a student/teacher/parent/staff, just click through the Education Store link)
Apple Refurb 1019+86 = 1105 AppleCare from Amazon 211 Total $1316
When the Back to School promotion begins then you should also get a free iPod Touch or perhaps $200 discount on a new iPad. But only if you buy from the Apple Store and only new Macs, not refurbs. I would put that into the equation.
Micro Center 999+85 = 1084 Applecare from Amazon 211 Total $1295
MacMall 1137 (no sales tax) Applecare/Amazon 211 Total $1348
Amazon exactly the same as MacMall Total $1348
If you have a Micro Center nearby then that's the absolute cheapest. But, you lose the freebie Touch on the Back to School promotion. There are probably some cheaper places for Applecare than Amazon but I haven't researched that too well.
My choice is the Education Store when the Back to School promotion begins. I don't have a Micro Center near me but I would choose Education anyway, since the free Touch has to be worth more than the $80 difference. Also, Micro Center doesn't have the greatest reputation for customer service (in case you want to return it), so that's another plus for buying direct from Apple.
Apple refurbs have excellent reputations, so that's also a good way to go if you don't have a Micro Center, although for $32 difference I would be tempted to go new from Amazon.
Even though these are numbers for 13" I hope they're helpful.