On Linux, pick the color of the slider's thumbpart from the GTK theme....

chrome/renderer/render_view.cc

Index: chrome/renderer/render_view.cc
===================================================================
--- chrome/renderer/render_view.cc	(revision 34028)
+++ chrome/renderer/render_view.cc	(working copy)
@@ -3210,6 +3210,12 @@
 #if defined(OS_LINUX) && !defined(TOOLKIT_VIEWS)
   WebColorName name = WebKit::WebColorWebkitFocusRingColor;
   WebKit::setNamedColors(&name, &renderer_prefs.focus_ring_color, 1);
+
+  if (webview())
+    webview()->setScrollbarColors(
+        renderer_prefs.thumb_inactive_color,
+        renderer_prefs.thumb_active_color,
+        renderer_prefs.track_color);
 #endif
 }