Both men became their party's candidate for President at the expense of more-heavily favored candidate. Hillary Clinton was the front-runner for a long time before Obama beat her in the primary. Lincoln beat out Republican heavyweight William Henry Seward. The Republican convention thought Seward's seemingly radical stance on slavery made him unlikely to win. Coincidentally, both Clinton and Seward were senators from New York when they ran for President, and both were forced to campaign for the person who just beat them.
Well, now add one other comparison. Abraham Lincoln appointed William Henry Seward to be his Secretary of State. Barack Obama has tipped Hillary Clinton to be his Secretary of State.
Of course, throughout the Obama presidency, I will be on the lookout for more comparisons to the Lincoln administration. You'll be the first to know if I find any.