The first commercially viable GUI on commodity hardware sounds pretty innovative to me, and that's just the tip of the iceberg.
For me, though the biggest 'technical' innovation that Apple has consistently delivered on is in making technology usable in everyday life.
Sure, it's not hard-core cryptography or massively parallel search-algorithms. But making devices and interfaces that are beautiful and enjoyable to use on a daily basis is incredibly difficult, and ranks just as high on my list as PageRank or Cassandra.
Thanks to Apple (and Jobs), I've got technology from Star Trek sitting in my pocket -- an iPhone. It wasn't the first smartphone by a mile, but it was the first that was genuinely useful to everybody, which is why every other phone on the market has followed Apple's lead in interface design.
Call that 'marketing' if you will, but all of that 'marketing' has made the world a better place for a very large number of people in a direct and measurable way.