The damage will be in PR. He's an almost unrivalled corporate showman, and few companies are as associated with their CEO as Apple. Whoever gives keynotes in the future would be wise to develop their own style rather than copy his. There may also be collateral damage in ruthlessness and vision - we constantly hear how he drives new products, and kills off "failures" early. However, the more I read recent interviews with anonymous Apple employees, the more I see he seems to have reformed the company in his image. It's impossible to gauge how much actual presence he's had over the last few years, and it seems quite likely the press have over-egged his effect. As long as his successor is not a radical corporate reformer, and is willing for a few years to be seen as an "Heir to Jobs", it seems likely to me things will roll on quite successfully.
I suspect Jobs will "retire" either this or next year. When they replace him, if they don't promote from within, then any CEO should: absolutely not engage in a massive expansion/race to the bottom; introduce change slowly rather than play with Apple like a new toy and; rely on the corporate team that's been built until they deeply understand what's working and what's not.
In many ways, Job's eventual departure (hopefully based on choice, rather than necessity) could be good for Apple. I firmly believe a little of his control freak nature could be sanded off the company to their advantage. They should drop the "Control for control's sake" direction they've been taking recently, and stay focused on the core corporate ethics that have bought them success - a high degree of perfectionism, technical risk taking, user focused design through everything, and a great marketing team. It won't be exactly the Apple of today, but given some of the…hostile decisions over the last 3 years, it might actually be an improvement.