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I always use brown extra large eggs, but I can't honestly say why I do this other than habit at this point. Are there any distinct advantages or disadvantages like flavor, shelf life, etc?

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Great question – that's been in the back of my mind for quite a while too! –  Owen S. Jul 10 '10 at 19:09
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Brown eggs are cheaper, at least where I live –  dassouki Aug 16 '10 at 11:20
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up vote 41 down vote accepted

The Egg Nutrition Center's FAQ page has an entry on this very topic. Basically, the color of the egg does not affect the egg's flavor, nutritional value, etc. It simply depends on the particular breed of chicken that lays the egg -- white eggs from white hens, brown eggs from brown hens.

It's also worth noting, as the ENC points out:

Generally, brown hens are larger and require more feed and therefore their eggs may be slightly higher priced.

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Donut must have meant: white eggs from white laying hens and brown eggs from brown laying hens. Leghorn hens lay white eggs. Their feathers can be all white, or all black, or mixed brown. –  papin Jul 13 '10 at 12:28
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In addition, there are breeds of chicken that lay greenish or bluish eggs -- these can often be found at farmer's markets. –  Martha F. Aug 12 '10 at 19:12
    
My dad could tell the different between a cooked white and brown egg by taste along. Although he was the only person I knew that could. Additionally it wasn't a double-blind test, so maybe my mom was tipping him off. –  Jim McKeeth Jan 6 '11 at 6:35
    
Bron eggs cost more because people think they are good for you (cf brown bread) and so stores can charge more –  Martin Beckett Apr 1 '11 at 16:12
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Cosmetic only, based on the breed of the chicken. When I was growing up we had some South American Aracaña chickens. Besides being able to fly, the two hens laid pale yellow and green eggs. Kind of like pre-colored Easter eggs!

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There difference between white and brown eggs is purely cosmetic. There is no nutritional or taste difference.

Brown eggs, IMO, look cooler, though. ;-)

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The only difference you might notice would be if you free range eggs instead of factory farm eggs. There is a slight yolk color difference and I think a slightly better flavor. Mine come in a range of colors including green, brown, and white.

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Fresh eggs from a free range chicken are to die for. Once you try em you will never go back to grocery store eggs again! –  Chris Sep 14 '10 at 14:46
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