If I were a betting man, I'd bet that the Mandate portion of Obamacare is struck down.
A lot of the rest of it will fall under the regulatory power of the Federal Government. It's a bit dicey, as that regulatory power falls under Interstate Commerce and Healthcare is actually regulated by the State to the point you can't actually DO business cross state lines when it comes to health care, but I'm betting you'll see the Supreme Court uphold a lot of the finer details.
Some of it, like the Exchanges, won't even be addressed as those are well within Federal power.
Once the Mandate is struck down though, that's going to cut the heart out of this bill. The Mandate was the one pay off for the Health Insurance Providers that might have got them to bring down costs. Without it you'll see the Insurance Companies saddled with more regulation and less incentive to bring down cost.
However, the most onorous parts of the bill aren't supposed to kick in until Obama is safely re-elected. If we can instead elect a President committed to repealing Obamacare in its entirety and strengthen Congress with people who will support him/her in that, then we can start over and do some real healthcare reform. And that won't involve the federal government taking over control of 16% of the economy.