I had heard the Permian extinction was caused by continental drift. All the shallow seas where Paleozoic Era life flourished were closed, pushed up and drained. Or so I heard.
The theories I have heard recently seem to focus on methane, although what the source of the methane was ranges from volcanism to methane hydrates to microbes. Many also think that the extinctions occurred in waves over a period of time, rather than one sudden event.