OK, here's john's patch plus my sync stuff.

chrome/browser/ui/browser_browsertest.cc

Index: chrome/browser/ui/browser_browsertest.cc
diff --git a/chrome/browser/ui/browser_browsertest.cc b/chrome/browser/ui/browser_browsertest.cc
index 56e4de271739b771d3bc4a2c183f4af92dd480d3..3908a6aae9a579ee6ae8f5d83f5b96459ff9627a 100644
--- a/chrome/browser/ui/browser_browsertest.cc
+++ b/chrome/browser/ui/browser_browsertest.cc
@@ -1077,7 +1077,13 @@ IN_PROC_BROWSER_TEST_F(BrowserTest, RestorePinnedTabs) {
 
 // This test verifies we don't crash when closing the last window and the app
 // menu is showing.
-IN_PROC_BROWSER_TEST_F(BrowserTest, CloseWithAppMenuOpen) {
+// TODO(linux_aura) http://crbug.com/163931
+#if defined(OS_LINUX) && !defined(OS_CHROMEOS) && defined(USE_AURA)
+#define MAYBE_CloseWithAppMenuOpen DISABLED_CloseWithAppMenuOpen
+#else
+#define MAYBE_CloseWithAppMenuOpen CloseWithAppMenuOpen
+#endif
+IN_PROC_BROWSER_TEST_F(BrowserTest, MAYBE_CloseWithAppMenuOpen) {
   if (browser_defaults::kBrowserAliveWithNoWindows)
     return;
 
@@ -1951,7 +1957,13 @@ IN_PROC_BROWSER_TEST_F(ClickModifierTest, WindowOpenControlShiftClickTest) {
 }
 
 // Middle-clicks open in a background tab.
-IN_PROC_BROWSER_TEST_F(ClickModifierTest, WindowOpenMiddleClickTest) {
+// TODO(linux_aura) http://crbug.com/163931
+#if defined(OS_LINUX) && !defined(OS_CHROMEOS) && defined(USE_AURA)
+#define MAYBE_WindowOpenMiddleClickTest DISABLED_WindowOpenMiddleClickTest
+#else
+#define MAYBE_WindowOpenMiddleClickTest WindowOpenMiddleClickTest
+#endif
+IN_PROC_BROWSER_TEST_F(ClickModifierTest, MAYBE_WindowOpenMiddleClickTest) {
   int modifiers = 0;
   WebKit::WebMouseEvent::Button button = WebKit::WebMouseEvent::ButtonMiddle;
   WindowOpenDisposition disposition = NEW_BACKGROUND_TAB;
@@ -2014,7 +2026,13 @@ IN_PROC_BROWSER_TEST_F(ClickModifierTest, HrefControlShiftClickTest) {
 }
 
 // Middle-clicks open in a background tab.
-IN_PROC_BROWSER_TEST_F(ClickModifierTest, HrefMiddleClickTest) {
+// TODO(linux_aura) http://crbug.com/163931
+#if defined(OS_LINUX) && !defined(OS_CHROMEOS) && defined(USE_AURA)
+#define MAYBE_HrefMiddleClickTest DISABLED_HrefMiddleClickTest
+#else
+#define MAYBE_HrefMiddleClickTest HrefMiddleClickTest
+#endif
+IN_PROC_BROWSER_TEST_F(ClickModifierTest, MAYBE_HrefMiddleClickTest) {
   int modifiers = 0;
   WebKit::WebMouseEvent::Button button = WebKit::WebMouseEvent::ButtonMiddle;
   WindowOpenDisposition disposition = NEW_BACKGROUND_TAB;