From https://github.com/bitcoin/bitcoin/pull/107

Following Ubuntu's method of distribution, here's how I think Bitcoin should be offered:

1) There should be 2 packages:
bitcoin-x.y.z
bitcoin64-x.y.z
(distributing 32 bit and 64 bit builds respectively)
2) For both of these packages, bitcoin is in the top level directory.
3) bitcoind is 'hidden' in a subdirectory (like bin)
4) The main page has 2 download links like:

Bitcoin for Linux (Recommended)
Bitcoin for Linux (64 bit)

The current structure is confusing for non-technical users. See http://bitcointalk.org/index.php?topic=3904.0 for the reason why.

An alternative proposal is in the first url at the start of this post.

Why are there 2 windows packages (zip and exe) btw?