How about something with hail? I had some massive hail here the other day and I thought I was being bombarded by the US military.
I don't know how weather works or how these changes might work, but maybe these could be some possible effects of bad or good weather.
1. Rain (flying increases hail damage)
a. drizzle (no effect)
b. steady downpour (scan doesn't work, can't sleep)
c. thunderstorm (scan doesn't work, can't sleep, possible lightning or tornado)
d. hail (same as above, also causes 1-10 damage)
2. Wind (flying increases chances of being swept)
a. slight breeze (no effect)
b. blustery (rare random movement to an adjacent room, can't sleep)
c. windstorm (strong chance for players to be swept every round, can't sleep)
d. gale (players swept, can't sleep, and damage from debris (increases if flying), 1-10 every round)
3. Snow
a. flurries (no effect)
b. snowstorm (scan doesn't work, can't sleep)
c. blizzard (freezing damage depends on number of eq slots filled - If a player is naked, then they receive the most damage 10-20. They take none if all slots are full. Avians are ok with less eq, since they have feathers.)
4. magic weather
a. color swirl (no real effect, just random colors in the sky)
b. magic storm (chance of a random spell being cast on a player, could be good or bad)
c. magic vortex (same as above, can't sleep, drains mana slightly)
5. Fog
a. mist (scan doesn't work)
b. pea soup (cannot see room description or objects)
6. Sunshine
a. partly cloudy (no effect)
b. balmy (hp/mana regeneration increases slightly, 10-20 bonus)
c. tropical (hp/mana regeneration increases even more, 30-40)
d. hot (hp/mana bonus goes back down to slight, or no effect)
e. blazing (no effect, or slight damage 1-10 every few rounds)
If someone is inside of a container, then they feel none of the effects from weather, good or bad, except tornado. Tornadoes have a chance of destroying vehicles or tents. Unsheltered players receive incredible damage from lightning and tornadoes. On the plus side, these phenomena are rare.
I do like Enter's idea of changing seasons. Each season (group of months) has a certain weather type that is predominant, and one that is rare. Chances of weather increase or decrease accordingly.
Winter: +Snow -Sunshine
Spring: +Rain -Wind?
Summer: +Sunshine -Snow
Fall: +Wind -Rain?
The builder has the option of keeping or removing any weather type to his/her area. For instance, Joey is building an area with two different climates. One part of his area it is a valley, the other is a mountaintop. Joey decides that it can snow on his mountain, but is too cold for rain or sunshine. He adds the appropriate flags to his mountain rooms that indicate no rain or sunshine (the default includes all weather types). His valley rooms can receive all kinds of weather so he leaves them alone.
These are merely suggestions. Change them or ignore them.

The stars brightly shine upon our world, a constant reminder of our origin. We are stars.