The latest issue of Wired magazine has a chart of the top 30 molecular shapes in the Chemical Abstracts Service database of more than 24 million compounds. Their definition of shape is based on rings and linkers which connect the rings, nothing else is considered: not the side chains attached to the rings or their connectors, presence of multiple bonds, or the elements involved.
As they point out many of the compounds listed are naturally occuring, or synthesized with natural compounds as the starting point or inspiration. Not surprisingly, the most common shape they identify is a hexagon and the second most common is the pentagon. The preferred bond angles for most organic compounds are around either 109 degrees or 120 degrees. Four- and three-membered rings (squares and triangles) aren't that common in nature - they do not appear in any of the top 30 shapes. These small rings have much smaller bond angles, and feel a lot of strain when forced to have such compressed bond angles. 5- and 6-membered rings have effectively zero ring strain and are very common in nature. Larger rings can also have ring strain issues.
About half of the top 30 shapes include a pentagon, but there is one or more hexagons in every one of the top 30 shapes except for shape #2 which is a simple pentagon.
Wired: Molecular Frameworks, the Building Blocks of All Life