When Apple Inc.’s (AAPL) Steve Jobs took six months’ medical leave this year, COO Timothy Cook ran the company. And now Cook is reaping the rewards.

A new Apple filing with the Securities and Exchange Commission shows Cook will have earned $800,000 in salary for 2009, received a cash bonus of $800,000 and been awarded $12.3 million in stock compensation.

But Cook isn’t the only Apple exec ending the year on a high financial note. CFO Peter Oppenheimer more than doubled his stock award to $8.8 million and his salary jumped to $700,000, up from $600,000. His cash bonus totaled $700,000 as well.

Meanwhile, Robert Mansfield, who heads the Mac hardware engineering division, is getting $12.2 million worth of 2009 stock awards, along with a $600,000 salary and $537,000 bonus. iPhone lead Scott Forestall, on the other hand, earned $12 million in stock, $600,000 in salary and $275,000 for a bonus.

Steve Jobs took his typical $1 salary and $1 bonus. He owns 5.5 million shares of Apple stock, though, and with shares near their 52-week high of $213.95, is far from destitute.