We recommend using a CSS preprocessor like LESS, SASS or Stylus to take care of CSS3 vendor prefixes. Besides making your code easier to write, a properly executed solution will help you maintain vendor prefixes over time, as CSS3 standard goes mainstream.
Take a look at our choosing a CSS preprocessor article.
If you want CSS3 prefixing to be absolutely transparent, Stylus + Nib do that out of the box. Stylus might not be for everyone, though; we recommend Compass as your default choice, please read that article mentioned above.
On v2.3.8 or earlier, prefix-free breaks the live CSS preview function.