Doing about 5 minutes of research on the interwebs, I found that really, there seems to be only two reasons that companies use green bottles: First, it is all about marketing the product. Yep, nevermind that the beer has that skunky effect, it looks good in green. Second, the company may actually be going for that effect, as some people actually like the skunk. For those people I ask, "Where were you when the skunk fell into my window well last spring?"
The best information I got was from, of all places, a Yahoo! Answers post answering the question, "Do green bottles really make beer skunky?":
Not the green bolttes but UV light. Brown bottles do the best at filtering out the UV light. Heineken beer was once known for this defect and built its world reputation on peoples' ignorance of it. Many people thought the "skunkiness" as normal and a quality beer aroma and flavor...
Lots of really decent information in that whole answer.
I'm not really a fan, honestly, of most beers in green bottles, but there are a few pilsners that I think I would enjoy a whole lot more if they were only in brown bottles. Jever, Czechvar (Budvar), and Pilsner Urquell taste so much cleaner from the tap.
As far as Rolling Rock, Heineken, Stella Artois, and Beck's go, they can keep them in the green bottles, since I don't