For playing around or to accompany tools/systems without an assets pipeline, Lea Verou's prefixfree[0] works very well, it does not require a compilation/munging phase and only generates the necessary prefixes for the browser it's run into. Really quite convenient.

[0] http://leaverou.github.io/prefixfree/

I'm working on a major redesign right now and working heavily with Flexbox. Between all the prefixes and the display: table fallbacks I'm using for old IE, there's a lot to manage.

Autoprefixer's value really becomes obvious when dealing with Flexbox. Flexbox is unique because it's not just vendor prefixes, but two previous specs that you need to manage. I really couldn't build a large site without it.