It seems like Amazon has better prices on their digital movies but I want to get the best quality even if it means paying a few extra bucks.
I haven't found Amazon to be any cheaper in most cases, they're at least as likely to be more expensive than iTunes in fact. I just checked as a sample all the 2012 Oscar best-picture nominees - other than Amour, which isn't available from either, all were exactly the same price for HD from Amazon and iTunes.
So then I checked some older films - the best picture winners from 1950, 1960, 1970, 1980, 1990, 2000, and 2010 - again in HD for each.
1950 - All About Eve - Amazon $19.99, iTunes $14.99
1960 - The Apartment - Amazon n/a, iTunes $14.99 (rental price same on both)
1970 - Patton - Amazon $9.99, iTunes $14.99
1980 - Ordinary People - Amazon $19.99, iTunes $9.99
1990 - Dances with Wolves - Amazon $14.99, iTunes n/a (rental price same on both)
2000 - Gladiator - Amazon $17.99, iTunes $17.99
2010 - The King's Speech - Amazon $9.99, iTunes $9.99
So Amazon cheaper on one, iTunes cheaper on two. Each service missing one title for purchase.
Between the two I prefer the downloaded file approach of iTunes. I don't need to worry about connection speed, I can transfer the file to my laptop or iPad to watch offline, I don't have to worry that Amazon's servers may be having problems when I want to watch a movie. However if you have Kindle Fire or Google TV or other hardware that doesn't play well with iTunes, that could affect your decision.
As often as not I'll end up buying the physical DVD or Blu-Ray and ripping it. For example Gladiator is $17.99 from iTunes or Amazon instant video, but Amazon has the Blu-Ray for $14.99 with free 2nd day shipping as an Amazon Prime member. That just seems silly to me but there it is.