Certainly, there's no doubt that His Steveness radically influenced Apple. While other PC vendors primarily saw themselves as integrators of available technologies, Apple saw itself as an innovator and they continue to redesign anything and everything to achieve their goals. Sometimes, this led in stupid directions (e.g., proprietary five-sided screw heads) and sometimes brilliant (e.g., the MagSafe connector).
Presumably, His Steveness leaves behind a huge stamp on Apple's culture that will impact how the company designs products for years to come. What I imagine will be missing, in the shorter term, is His Steveness's prowess at negotiating big deals. Nonetheless, Apple now has such a commanding market presence that they have a lot more power to drive the agenda. They'll do fine.
I imagine that Jobs would rather do nothing more than keep running Apple. I believe he's said as much, and all the public discussions are treating his stepping down as equivalent to his passing away. He's not dead yet. Maybe he'll have something really interesting planned as a last hurrah. Maybe something charitable. Maybe something outrageous. We'll see.