Websites have incredibly evolved over the past years, more and more code is written for the client side and less on the server side.
Unfortunately Google Bot was still stuck in the nineties, reading pages as they were a block of pure HTML. Today this is going to change, as Google today announced:
That's really great news, a lot of us have waited for something like this for a long time. But this will also introduce a big amount of problems an leaves me with a lot of unanswered questions. But there is hope, the webmaster tools will get a new tool and I guess Google will update it's webmaster documentation soon, to give us hints about how we should adapt our websites to handle this totally new situation:
"To make things easier to debug, we're currently working on a tool for helping webmasters better understand how Google renders their site."
Read the official google webmaster central blog post for more.