In the winter....
On a trailer, always leave the motor down, (verticle).
In a slip, (salt water) we also leave the motor in the down position, (submerged). Usually starting in December, (in recent years anyway) when air temps near the shore start to drop below freezing. The water temps are usually still higher than air temp, so it's safer to leave it down. Salt water starts to freeze around 28f too, I believe. So that's another safety margine.
If it got really cold over night and you forgot to leave the motor down, you should lower the motor, and wait a few minutes for the warmer salt water to thaw any water that may have froze in the lower unit. This is no garrantee, but it's a another method people use. But again, safest thig is to leave it down.
In fresh water... you better have your boat out by then. :wink:
I also do as Josh S suggests for winter storage. Short length of garden hose and a funnel, connected to the muffs. I run about 3/4's of a gallon into the muffs, after the engine has been running and warmed up. Usually after about a half a gallon, you'll see it exiting the pi$$er. I don't think it's necessary, but it sure can't hurt. Just a little extra piece of mind.