Here are some highlights of lessons learned.

He takes a pause.

The first thing Jobs does is probably the hardest.
He takes a pause, sits in silence ...
And thinks.
In what seems like an eternity to the audience (and in reality lasted about 10 seconds), Jobs takes a sip of water and reflects on both the criticism and the question.
"You know," he begins his reply. "You can please some of the people some of the time, but ... "
Another pause, this time for about eight seconds.
I've written extensively on the value of the pause--a technique that involves taking a few moments (or sometimes more) to stop and think before taking action. The pause is so valuable because it allows you to get your emotions under control and think things through before you say or do something that you'll regret.
Jobs's initial pause gives him the time he needs to compose himself and come back with a thoughtful and remarkable response.

He agrees with his accuser.

"One of the hardest things when you're trying to effect change is that--people like this gentleman--are right! ...In some areas," explains Jobs.
For years, psychologists and other academics have argued that the best way to change a person's mind is not to attack their position but, rather, to find common ground.
Jobs does this perfectly by acknowledging that this man is (gasp) right! There are surely features with OpenDoc (the program in question) that he isn't familiar with.
But becoming familiar with every feature of every app is not the CEO's job, as he goes on to explain.

He helps everyone see the big picture.

Jobs goes on to outline his role at Apple: It's not to know the ins and outs of every piece of software. Rather, it's to see the big picture, to reiterate the vision, and to keep everyone on course:
"The hardest thing is: How does that fit into a cohesive, larger vision, that's going to allow you to sell eight billion dollars, 10 billion dollars of product a year? And one of the things I've always found is that you've got to start with the customer experience and work backwards to the technology. You can't start with the technology and try to figure out where you're going to try to sell it."
This extremely compelling vision of working backwards from customer experience may have been innovative at the time ...
But, as history proved, it was right.

He uses vulnerability to his advantage.

In reference to working back to the customer, Jobs continues:
"And I've made this mistake probably more than anybody else in this room. And I've got the scar tissue to prove it. And I know that it's the case."
Jobs not only explains his vision, he uses his own learnings to help establish his credibility. In essence, he begs stakeholders (and shareholders) to benefit from his experience.

He praises his people.

"There are a whole lot of people working super, super hard right now at Apple," Jobs exclaims. He names a few examples, before going on to credit the whole team, literally "hundreds of people."
"They're doing their best," says Jobs.
With these words, Jobs gets behind his team. He acknowledges them. He praises them.
He lets them know he's got their backs.
This inspires the team (and others) to get behind him, too.

He finishes strong.

Jobs's final words are motivating.
"Some mistakes will be made, by the way. Some mistakes will be made along the way. And that's good. Because at least some decisions are being made along the way. And we'll find the mistakes, and we'll fix them," Jobs says to applause.
He then comes full circle to the original questioner:
"Mistakes will be made ... some people will not know what they're talking about, but I think it is so much better than where things were not very long ago.
"And I think we're going to get there."