For the most compatibility with iPods and iPhones, use the Universal preset. If you don't think you'll ever want to transfer your media to one of those devices, the Apple TV preset will result in slightly smaller file sizes for the same quality.
If your only ever gonna use them on your mac mini and plex then why not use one of the high profile presets such as Television or Film. This will enable features that the AppleTV dosn't support and should give a better encode.