I'm surprised that this hasn't been discussed to death already (or has it? didn't find much on it).
the possibilites are endless, and i'm too lazy to list them all atm ^^
for starters:
- rain has a positive effect on farmig/growth
- rain can create small pools of water and fill a cointainer with water
- rain and temperature drop at night has a negative effect on players
- negative effects can be cancelled with campfires, shelter, clothing, etc.
- thunderstorms have a bigger negative effect and cause damage