Add in an invisible space:
1. Type in the following command into terminal: defaults write com.apple.dock persistent-apps -array-add '{tile-data={}; tile-type="spacer-tile";}'
2. Next insert the command: killall Dock
Minimize Applications into their icon:
1. Type in the command: defaults write com.apple.dock minimize-to-application -bool yes
2. Type in the command: killall Dock
Now your dock will be a little less cluttered thanks to these two simple commands.