Sounds like you've got your Finder set to show a bunch of stuff that's normally hidden. These two Terminal commands will get rid of the .DS_Store files being visible:
defaults write com.apple.finder AppleShowAllFiles -boolean false
killall Finder
As for /home and /net, I'm not sure why those are showing up. On my system, they're there, but not displayed by the Finder. It might have something to do with the AppleShowAllFiles setting being turned on, which the two commands above should take care of, but if they still show up after that, you might want to just try trashing the Finder's preference file, which is in the following location:
Home -> Library -> Preferences -> com.apple.finder.plist
Then log out and back in again, and see if the problem goes away.