What are the most strange/sophisticated/surprising/deeply hidden software vulnerabilities or exploits you have ever seen? Places in code where you thought that there is no danger hidden, but were wrong?
[To clarify: Everybody knows SQL injections, XSS or buffer overflows - bugs which often result from careless coding. But things like Ken Thompson hidden trojan (Reflections on Trusting Trust: http://cm.bell-labs.com/who/ken/trust.html), recent NULL dereference vulnerability in Linux kernel (http://isc.sans.org/diary.html?storyid=6820), or a complex attack on RNG using denial of service (http://news.ycombinator.com/item?id=639976) have disturbed me greatly.]
Update: Thanks all for answers, they were great. I had hard choice. Ultimately I decided to award the bounty to side channel/power monitoring attack. Nevertheless, all your answers combined show that I have to learn more about security, since it's a really deep subject :).
Somehow related: Best real "computer crime"?