I did my BA online at ASU; while my transcript doesn't say that it was online, it's pretty obvious because I live on the East Coast. I realize it's not Harvard, but I was able to get into Johns Hopkins. They looked at my college transcript (I graduated Summa Cum Laude with a 4.0 GPA), an essay, my resume, and two recommendations. Of course, I'm doing the program online BUT the same program is also offered on-campus.
BA - History, Arizona State University
MS - Organizational Leadership, Johns Hopkins University (in progress)
MS - Organizational Leadership, Johns Hopkins University (in progress)