Well, this is an informative post, not a question to ask, so feel free to elaborate and move it accross the board if I managed to post it to a wrong forum.
It seems like in the battle of linux to dominate desktop market and introduction of thin clients to run windows applications natively linux has undermind its security a big time, now there are two articles on securityforum which talk about something called reverse engineering, the likes linux has done to get itself familiar with NTFS, but now it is trojan horses that get reverse engineered with aid of Wine and Cygwin. So read on,
Part I
http://online.securityfocus.com/infocus/1637
Part II
http://online.securityfocus.com/infocus/1641
Note: I assume you'll use it as a learning material on how to make your linux adventures safer.