Sierra Nevada definitely uses brown bottles- those shorties are my faves. You're probably thinking of Newcastle, also Corona and other mexi-lagers. Really, all beer needs to be kept out of the light, including those in brown bottles, but it adds an extra layer of protection. Brown>green>clear. Most of my bottles stay in crates and covered with a sheet/blanket while conditioning so I'd have no qualms using those bottles, I just don't buy any beer that comes in them.
The big guys use the other bottles for presentation, because they sell their beer based on marketing and shelf appeal, not on taste like the little guys. Every bottle of Corona or Heineken I've ever had has been skunked pretty badly, most people think it's part of the flavor profile, but a Heineken out of a can is really quite a nice lager (poured into a glass, of course). BJCP teachers do this all the time for demos, skunk beer intentionally to give tasters so that people know what it tastes like.