As stated in the title, MathOverflow is a .net website, unlike every other site I've seen in the SE network, which are all .com sites. Why is MathOverflow the sole .net site of Stack Exchange?
The main reason is that MathOverflow was started by Anton Geraschenko, who was a graduate student in mathematics at the time, not a StackExchange employee. The process for starting sites with the StackExchange software at the time was not the same as it is now, and Anton was the one who registered the domain. The site become more closely integrated with the rest of the StackExchange universe in 2013, but the domain remains the same. You can read a brief prehistory by Anton on this page.