Whether it's best to leave the toilet seat up or down is a moot point in our house. For at our place everybody knows the toilet lid itself must be closed prior to flushing. It's about containing the germs as well as making the bathroom look as civilised as possible.
Just think: every time you flush the loo it stirs up all the nasty bugs inside and allows them to float invisibly around the bathroom. And that's not an old wives' tale either. Even the health professionals agree lids help prevent the spread of germs. As quoted at nursingtimes.net in Nursing director: put toilet lid down when flushing: "Leaving the lavatory lid up can allow a cloud of bacteria to explode into the air, settling on nearby surfaces, including towels, flannels and, more worryingly, toothbrushes."
Evidently, research at Leeds Teaching Hospital Trust found that "bacteria could be transported up to 10 inches above a toilet seat when left open and remain in the air for up to an hour and a half."
I received this information gladly since I've long been insisting on this protocol for the exact same reason. Other toilet-related issues pale into insignificance in the face of this most pressing point.
You can forget such trivialities as whether the seat should be up or down (although, for the record, the answer is, obviously: down) and how the toilet paper should be installed on the toilet roll holder (clearly, the leading edge of the toilet paper should be farthest from the wall - and, ergo, most readily accessible to the user). The twenty-first century's bog standard dilemma is all about lid position. And it's a no brainer, really.