Skintone pantyhose are definetly outdated, particularly with flats.
I do wear trouser socks, in color to match the shoe, and preferably with interesting textures or patterns. But I wouldn't wear them with ballet flats, since the vamp is so low, and the lack of arch support or a heel can cause unattractive bagging or coloring around the ankles. I would say ballet flats with trouser socks is ... kind of a dowdy look, I'm afraid.
I would wear them instead with a more structured shoe that has a bit of a heel and a higher vamp. For example something like this:
http://www.zappos.com/n/p/dp/51982234/c/89.html
Worn with dress slacks (not a skirt)... would look adorable with trouser socks like this:
http://www.barenecessities.com.....02665-_-NA
The pretty pattern peaking out just takes it all up a notch.
I do think you can also get away with colored trouser socks and pumps, but it's trickier. Not any pump works with this. I think it works best with rounded-toe pumps that have more substantial, chunkier heels. For example, I have these shoes:
http://ecx.images-amazon.com/i.....AA280_.jpg
And I would wear these with trouser socks in a matching gray, under slacks, probably gray slacks, to get that one long lean leg line.