0.1uF is probably the most common, though I have seen 0.01uF used as well. Larger values (6.8uF, 10uF, etc) are used to filter out lower frequencies. It all depends on your exact circuit, where it will be used, what you are using for a power supply, and so on.
I generally just use a 0.1uF capacitor directly across the power pins of the microcontroller and don't have a problem. Just make sure you put the cap as close as you possibly can to the power pins when laying out your board.
Here is a tutorial on bypass capacitors:
There they discuss different types, why they're needed, how they're used, and how their values are calculated. Hopefully this helps =)
EDIT: Intersil also created a document to help determine which capacitors to use. I found this while reading through the previous link: