Add my vote to the "save the little moons" petition. I like the little buggers too.
Since often they are only good for one facility I like to use it for a resupply depot. Then I don't waste a slot on the planet. Also, when playing humans you can sometimes use them for "stealth outPosts" since nothing shows up on the main screen as long as you haven't colonized the main planet. Of course, you can't fake out the AI that way.
Has anyone run across alien ruins or tech on moons? If not, this would be a cool mod to make.