I had customized my Error Stripe Mark for Unused symbol to be a grey line and Deprecated symbol to be a black line to match the decoration in the editor pane.
Before I had done this, there were a number of times when I would see yellow stripes in the gutter for the code visbile in the editor pane, and I would search around looking for what was highlighted in yellow. In took me a few seconds to realize that it was the Unused Symbols which were greyed out.
I like how the editor styles the Unused symbol (greyed out) and Deprecated symbol (strikethrough), so I adjusted the error stripe to match so it is consistent. (See attached screenshot)
I would recommend Jetbrains do this for all of the errors and warnings.
Related Thread: http://www.intellij.net/forums/thread.jsp?forum=22&thread=178944