I don't think it will be ever done. Look at other platforms, such as Windows - you can install various games that exist in Steam library (the ones from the humble bundle too) but you can't "link" them to Steam to appear as regular Steam games. The same situation is here.
The Steam versions require integration with the Steamworks API for the sake of authentication, validation, and achievements (et al). The functionality would be limited in those regards.
The closest thing you can do is Games->Add a Non-Steam Game to My Library...
I'm closing this feature request.
Nothing extracted yet.
Some of the recent Humble Bundle games can be downloaded through PPAs, would it be possible for Steam to use these instead of downloading a (possible) second copy?
I know alternately I could download them manually through the PPAs then add them as an external app via steam, but this suggestion would streamline that a bit.
Thanks.