Usually, this is an indication of either:

1. A program that won't terminate, or

2. (more common in my experience) a driver that has lost control of a device. This could be something like a removable USB device that you removed without doing the "remove hardware" thing in the task bar. Most of the time you can remove USB hardware and get away with it. Sometimes you can't.

Sometimes, if you hit Ctl-Alt-Del, you'll get the task manager brought up to you and you can discover what is holding up the system (if a program). If it is a driver, you'd have to have programmer's tools to discover the driver that has hung an IO request. The system made a call into a driver, is waiting for the response from the driver, and the driver has gone to sleep and isn't timing the request. So the system just sits there, waiting for a response from the driver that will never come.

And you wonder what in the heck is taking so long. 

The application of a finger on the power switch is about the only solution I can recommend.