Another site I've seen in the wild Built with Bootstrap that was quite difficult to tell at first pass was Bright Nest. http://brightnest.com/

The Missouri Department of Conservation's E-Testing service for Hunter's Education also uses a customized version of Bootstrap, but it's pretty easy to tell it's Bootstrap. http://www.hunter-ed.com/missouri/

I'll add these to my follow up post on what sites do use bootstrap but you can't tell

Agreed. And the "Hero Unit". My buttons are blue (though I tried a darker blue than the standard look). They are still a dead giveaway.