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In my experience, as well as accounts of others' experiences, it seems that clear and green bottles are inferior to brown bottles for storing beer. I know this is due to the amount of light allowed through the bottle.
But why do breweries continue to use green and (especially) clear bottles? Why bother with a bottle that is more likely to allow beer to spoil?
Fully attributing the Berghoff Beer Blog for this interesting story (emphasis mine),
Around World War II, brown glass rose in demand and many companies had to forfeit their brown glass for their country. Unfortunately that meant companies with higher quality beers had to use clear glass, which made their beers look like cheaper, clear glass beers. Higher quality brewers’ solution was to sell their beer in green bottles so a consumer could tell the difference between a regular beer and a higher quality. The green beer bottle became a status symbol for many European breweries.
These days, there’s not much of a reason to sell a beer in a green bottle other than for marketing and aesthetic. Many companies use it to distinguish their beer from others. Of course, some beers have used green bottles for so long, it would seem silly to switch to a brown glass now.
Lucky for us, glass suppliers are able to apply clear, UV protected coats to glass that help keep beer fresh no matter what kind of bottle it is in. [...]
http://www.berghoffbeer.com/blog/what-does-the-color-of-your-beer-bottle-mean/
So, perhaps it's no longer the case that clear and green bottles are (noticeably) inferior to brown bottles!
Edit: I failed to find historical sources for the above claims, even some indication of higher demand for brown glass during World War II. However, the story seems widely believed today, true or not.
I would expect that companies which use clear bottles don't expect their product to see that much sunlight, or that they think their customers won't notice a little skunking if it does see any. Anecdotally, I typically associate clear bottles with the larger brewers (Coors, Budweiser), and I don't think of those beers as having much in the way of hops, the source of the isohumulones which, when combined with light, create the "skunk".
Wikipedia points out something interesting as well:
In some cases, such as Miller High Life, a hop extract that does not have isohumulones is used to bitter the beer so it cannot be 'lightstruck'.
