1.
Board Game: Dune
[Average Rating:7.63 Overall Rank:91]

A Spotlight on Games
United States Bay Area California
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Can't seem to find an image of it here, but there is a storm marker which plays a very important role.
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John Christopher
United States Edwards California
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TO THE CLOUD!
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3.
Board Game: Niagara
[Average Rating:6.59 Overall Rank:646]

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2004
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Kent Reuber
United States San Mateo California
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Both clouds and storm clouds are present.
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1999
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Rich Lallatin
United States John Day Oregon
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You have to manuever around the clouds.
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patrick stevens
United States Los Angeles California
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The Brain Cloud is from the movie Joe VS. the Volcano.
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Friedemann Friese
Germany Bremen Bremen
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1983
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patrick stevens
United States Los Angeles California
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This cloud steals your ships.
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1996
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1992
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1991
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1986
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Players create images with the cloud tiles.
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A Spotlight on Games
United States Bay Area California
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Don't have a picture of it handy, but the game does include a storms cloud counter which the balloons should avoid if they know what's good for them.
This list while not the same might be a good place to hunt for more entries.
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François Haffner
France Pierre-Bénite Rhône - Rhône-Alpes
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This game has a "Cloud variation for expert dwarves"
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2000
There's a big cloud on the left corner 
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2010
The tiles depict a cloudscape dotted with gemstones.
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2006
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- The Weather you like it or not list
- Weather-related games