Seat down, lid up.
As I mentioned in passing in the Toilet Seat Ups And Downs topic, I always sit, despite being male. I've never had good aim, and so standing is always more trouble than it's worth. The lid is usually up, because sometimes a bathroom trip is just too urgent to take the time to open the lid, but if I've made something particularly pungent, or if something seems not to be flushing properly, I'll put it down.