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

chrome/browser/ui/browser_browsertest.cc

 // Copyright (c) 2012 The Chromium Authors. All rights reserved.
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 
 #include <string>
 
 #include "base/bind.h"
 #include "base/compiler_specific.h"
 #include "base/file_path.h"
 #include "base/prefs/pref_service.h"
@@ skipping 1059 matching lines @@
             new_model->GetWebContentsAt(2)->GetURL());
 
   EXPECT_TRUE(
       extensions::TabHelper::FromWebContents(
           new_model->GetWebContentsAt(0))->extension_app() == extension_app);
 }
 #endif  // !defined(OS_CHROMEOS)
 
 // 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;
 
   // We need a message loop running for menus on windows.
   MessageLoop::current()->PostTask(
       FROM_HERE, base::Bind(&RunCloseWithAppMenuCallback, browser()));
 }
 
 #if !defined(OS_MACOSX)
 IN_PROC_BROWSER_TEST_F(BrowserTest, OpenAppWindowLikeNtp) {
@@ skipping 853 matching lines @@
 #else
   int modifiers = WebKit::WebInputEvent::ControlKey;
 #endif
   modifiers |= WebKit::WebInputEvent::ShiftKey;
   WebKit::WebMouseEvent::Button button = WebKit::WebMouseEvent::ButtonLeft;
   WindowOpenDisposition disposition = NEW_FOREGROUND_TAB;
   RunTest(browser(), GetWindowOpenURL(), modifiers, button, disposition);
 }
 
 // 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;
   RunTest(browser(), GetWindowOpenURL(), modifiers, button, disposition);
 }
 
 // Shift-middle-clicks open in a foreground tab.
 IN_PROC_BROWSER_TEST_F(ClickModifierTest, WindowOpenShiftMiddleClickTest) {
   int modifiers = WebKit::WebInputEvent::ShiftKey;
   WebKit::WebMouseEvent::Button button = WebKit::WebMouseEvent::ButtonMiddle;
@@ skipping 42 matching lines @@
 #else
   int modifiers = WebKit::WebInputEvent::ControlKey;
 #endif
   modifiers |= WebKit::WebInputEvent::ShiftKey;
   WebKit::WebMouseEvent::Button button = WebKit::WebMouseEvent::ButtonLeft;
   WindowOpenDisposition disposition = NEW_FOREGROUND_TAB;
   RunTest(browser(), GetHrefURL(), modifiers, button, disposition);
 }
 
 // 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;
   RunTest(browser(), GetHrefURL(), modifiers, button, disposition);
 }
 
 // Shift-middle-clicks open in a foreground tab.
 IN_PROC_BROWSER_TEST_F(ClickModifierTest, HrefShiftMiddleClickTest) {
   int modifiers = WebKit::WebInputEvent::ShiftKey;
   WebKit::WebMouseEvent::Button button = WebKit::WebMouseEvent::ButtonMiddle;
   WindowOpenDisposition disposition = NEW_FOREGROUND_TAB;
   RunTest(browser(), GetHrefURL(), modifiers, button, disposition);
 }