Jonathan ‘Wolf’ Rentzsch wrote a great article on Mac App Store vs Buying Direct, positing that application sandboxing tips the scale in buying direct.
I always prefer to buy direct because (using his words):
More Money Goes to the Developer: For a $10 application, only $7 goes to the developer when you buy it through the Mac App Store. For a direct purchase, it’s more on the order of $9.
The fact more developers weren’t encouraging customers to buy directly is a testament to how much Mac developers care about User Experience — they’re willing to forego the extra profit of selling direct to make things easier for their customers.
But this is a power user decision. I believe it’s App Store all the way for non-techies, family, friends and my mum’s computer.