The rain is soothing and refreshing as well as cleansing, suggesting a 'sin theory'.
In the Orientation video for The Swan, we're informed that The DHARMA Initiative was studying meteorology. Perhaps DHARMA is behind the sudden, heavy rainfall that occurs on the Island.
Sudden, heavy rains are common in tropical island environments.
In the Pilot Charlie remarks "Guys, is this normal? This 'End of the World' type weather?" A possible hint at the external conditions on the island are connected to what happens in the hatch.
The rain, like all environmental happenings on the island, is simulated.
The rain occurs whenever someone arrives or departs the Island via the bearing of 325 degrees
Yeah, probably right or really close. We've seen Frank fly through the storm (maelstrom?, tempest?) in order to go from island to real world. That sort of suggests this a portal. Also we know Desmond and Danielle landed on the island after their vessel went through a terrible storm.
Also, Ethan and Richard drug Juliet because the trip is rough, possibly alluding to a storm.
The rain comes at a certain time of day. When Locke and Boone are in the jungle locke stops and lifts up his arms and it begins to rain.
The sudden changes in the island's tidal and weather patterns is a side effect of the island constantly moving through space. Different parts of the ocean would have different current, tide, and weather patterns.
The sudden shift between heavy rain and blue skies may be a metaphor for the distinct personalities and effects of Jacob and the MiB—dark and stormy, light and bright. This would explain why towards the end of the show when Locke begins his war (316 and forward), this stark water cycle isn't seen again, as far as I can recall.