Facebook - Design was their early traction - clean and exclusive, with regimented testing in every release.
Apple - Built on incredible engineering and developers, leading case for vertical integration.
Google - Key innovation behind pagerank was scaling it with a node-based hosting architecture which was built by incredible engineers. Not to mention google maps which won on design alone and is becoming their #2 most important product.
Amazon - Innovations in shipping, distribution, and line automation are far more important than testing in the razor thin book marketplace that put them on the map.
Zappos - Ran out of steam here, probably a good combo of the above four :)
I see your point, that's what the companies are known for.
But in reality there are deeper innovations that are have powered those to the levels they are today - seems like each of the above GREAT companies above has at least 3 of the 5 areas hitting on all cylinders.