Scouts are small, fast ships with no attack capability (and not much in the way of defensive capabilities, either). What they are good at, though, is getting in and out of enemy starsystems and reporting back what they found.
Coupled with their ability to cloak (see below), scouts are perfect for learning about your neighbours and keep track of what they're up to.
The cloak upgrades makes the scout invisible to enemy radar. Additionally, if you set the fleet's stance to "Neutral" or "Passive" (so that it doesn't try to attack enemies), the scout will remain undetected on enemy stars. This is a great way to keep tabs on what your enemy is up to on neighbouring stars that your radar cannot reach.