Usually I don't pay a bit of attention to it. When I was running a sea-based game, Bad Weather was one of the most common encounters on the table, so it came up a couple of times. Sometimes, I'll roll luck for the group at the beginning of the day, and use that to determine how nice it is. If it's not nice, what's going on will be based on where they are and what time of year it is.
Getting much more detailed than that doesn't seem all that interesting to me, so I don't do it. If it's dramatically appropriate, guess what? It's raining. Or thunderstorming. Or whatever.