I've recently downloaded Eclipse 3.6, everything works fine, but there is one issue that really frustrates me. The highlight color of a currently selected item in a code assist popup is barely visible against white background. I've tried to mess with color settings, but it seems that there is no option for my needs. The line highlight color set in Windows color scheme is only used to highlight in a focused popup.
I believe it is hidden in another part of Preferences. I personally wanted to change the highlighted or currently selected line color, and could not find anything in Colors and Fonts. Ends up it was in...
General -> Editors -> Text Editors
And you just need to go through every option in the "Appearance color options" box there. One is "Current line highlight" and that fixed my problem. I hope it helps yours!