Several really important points:
Sanctions:Bush said that the sanctions weren't working because Hussein had still been in power. Kerry made the right point that in fact, the sanctions worked. Hussein had no WMDs and, by the way, the sanctions were not intended to take him out of power. Huge score for Kerry in my book.
Environment: Bush talked aout how the air is cleaner today than it was 4 years ago. That may be true, but it is despite his efforts, not because of them. He has relaxed standards on air and water pollution drastically.
Abortions: The other really telling part was during their discussion about partial birth abortions. Bush said and repeated, Kerry voted against it There's nothing else you need to know. Kerry explained his vote against it because it did not make necessary allowances in certain cases. I know many people see abortion as black and white, but there are a lot of gray shades there. Bush's inability to see or admit those shades is insane.
Accountability for the war: One other part that I found unbelievable was when Bush blamed his generals for not having enough people in Iraq. He said that he asked them point blank if they had enough troops to win to which they replied that they did. Kerry's response was that the general's job is to win the war; the president's is to win the peace. President Bush needs a sign on his desk that says, "The buck stops here."
Bush did make a strong point when Kerry went after him once again regarding the Osama-bin-Laden-holed-up-in-the-mountains-of-Tora-Bora-thing. He said, "It's a fundamental misunderstanding to say that the war on terror is only Osama bin Laden." Which neutralizes Kerry's point to some extent.
There was other give and take, but in my mind those were some of the most important points of debate two.