Question: How was this list generated, ie: how do you find out which hash number has a lot of bitcoins in it? I thought that was completely hidden.
See "Quantitative Analysis of the Full Bitcoin Transaction Graph”, a 2012 paper by Ron and Shamir. (Adi Shamir of “RSA".) Preprint available here: http://eprint.iacr.org/2012/584.pdf (The "Rich List” seems obviously inspired by this paper.)
Sadly that paper is pretty poor. It's adequate for informing someone bitcoin isn't anonymous though— but the bitcoin.org website also does that without being littered with basic misunderstandings of how Bitcoin works.