I had a interal disk that wouldn't show in the finder at all but was showing as mounted on disk utility. I could get to the disk through a file alias so I know the disk was there and working.
I tried numious posts including this one (http://www.daniweb.com/hardware-and-software/apple/mac-os-x/threads/94420/hard-drive-not-visible-mac-osx) with not luck.
I figured it must be a permissions problem, so I ran the termal command to show all hidden files (without the brackets):
(defaults write com.apple.Finder AppleShowAllFiles YES)
And Behold the HD was there as a hiddden file.
Then I found another termail command that makes hidden files not hidden:
chflags nohidden /path/to/the/file/to/change
and now my HD is back to normal - yay
Then made all hidden files back to hidden:
(defaults write com.apple.Finder AppleShowAllFiles NO)
Hope this helps someone