Why do some items in my Finder window appear grayed out?
The items you are seeing are invisible items. Names that start with a dot indicate the file should be hidden. If you changed finder to show hidden files, it will display them greyed out, but the files will work as normal. Besides having a name that starts with a dot, it is possible to set a special file attribute that will make finder hide the file. 

If you want to turn the showing of hidden files back off, one option is to use the terminal, open it and use this command: defaults write com.apple.finder AppleShowAllFiles NO and then log out and back in.