I just started a deal that takes advantage of this and I was surprised there were no topics discussing it.
Valve has been slowly rolling out the ability for publishers in the past couple of weeks to give their customers discounts on Steam game bundles if they already own part of the bundle. I believe the default normal behaviour is still "charge the full bundle price and provide no extra copies" but publishers can customise it if they choose to.
This is something I'm quite excited by as I have a Steam library of over 1000 titles and I've never found any game bundles attractive as I usually own one or more titles from them.
Here's an article from pcgamesn that has a bit more information.