diff --git a/Windows/DSoundStream.cpp b/Windows/DSoundStream.cpp
index f2e83c8b76..a5f46e6319 100644
--- a/Windows/DSoundStream.cpp
+++ b/Windows/DSoundStream.cpp
@@ -1,4 +1,4 @@
-#include <windows.h>
+#include "Common/CommonWindows.h"
 #include <dsound.h>
 
 #include "dsoundstream.h"	
diff --git a/Windows/DSoundStream.h b/Windows/DSoundStream.h
index 0a52c28e0a..9364d5b59d 100644
--- a/Windows/DSoundStream.h
+++ b/Windows/DSoundStream.h
@@ -1,7 +1,7 @@
 #ifndef __SOUNDSTREAM_H__
 #define __SOUNDSTREAM_H__
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 
 namespace DSound
 {
diff --git a/Windows/Debugger/BreakpointWindow.h b/Windows/Debugger/BreakpointWindow.h
index edb251d849..91121aa661 100644
--- a/Windows/Debugger/BreakpointWindow.h
+++ b/Windows/Debugger/BreakpointWindow.h
@@ -1,7 +1,7 @@
 #pragma once
-#include <windows.h>
+#include "Common/CommonWindows.h"
 #include "Common/CommonTypes.h"
-#include "../../Core/Debugger/DebugInterface.h"
+#include "Core/Debugger/DebugInterface.h"
 #include "Core/Debugger/Breakpoints.h"
 
 class BreakpointWindow
diff --git a/Windows/Debugger/CPURegsInterface.h b/Windows/Debugger/CPURegsInterface.h
index f31fed8f27..dbec96fedf 100644
--- a/Windows/Debugger/CPURegsInterface.h
+++ b/Windows/Debugger/CPURegsInterface.h
@@ -1,5 +1,5 @@
 
 #pragma once
 
-#include "../../Core/CPU.h"
+#include "Core/CPU.h"
 
diff --git a/Windows/Debugger/CtrlDisAsmView.cpp b/Windows/Debugger/CtrlDisAsmView.cpp
index b4b46c5dba..1960acdfc6 100644
--- a/Windows/Debugger/CtrlDisAsmView.cpp
+++ b/Windows/Debugger/CtrlDisAsmView.cpp
@@ -1,22 +1,22 @@
 // NOTE: Apologies for the quality of this code, this is really from pre-opensource Dolphin - that is, 2003.
 
-#include "../resource.h"
-#include "../../Core/MemMap.h"
-#include "../../Core/MIPS/JitCommon/JitCommon.h"
-#include "../W32Util/Misc.h"
-#include "../WndMainWindow.h"
-#include "../InputBox.h"
+#include "Windows/resource.h"
+#include "Core/MemMap.h"
+#include "Core/MIPS/JitCommon/JitCommon.h"
+#include "Windows/W32Util/Misc.h"
+#include "Windows/WndMainWindow.h"
+#include "Windows/InputBox.h"
 
 #include "Core/MIPS/MIPSAsm.h"
 #include "Core/Config.h"
-#include "CtrlDisAsmView.h"
-#include "Debugger_MemoryDlg.h"
-#include "DebuggerShared.h"
-#include "../../Core/Debugger/SymbolMap.h"
-#include "../../globals.h"
-#include "../main.h"
+#include "Windows/Debugger/CtrlDisAsmView.h"
+#include "Windows/Debugger/Debugger_MemoryDlg.h"
+#include "Windows/Debugger/DebuggerShared.h"
+#include "Core/Debugger/SymbolMap.h"
+#include "Globals.h"
+#include "Windows/main.h"
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 #include <tchar.h>
 #include <set>
 
diff --git a/Windows/Debugger/DebuggerShared.h b/Windows/Debugger/DebuggerShared.h
index 83ce04d7bb..c6109d5046 100644
--- a/Windows/Debugger/DebuggerShared.h
+++ b/Windows/Debugger/DebuggerShared.h
@@ -1,6 +1,6 @@
 #pragma once
-#include <Windows.h>
-#include "..\..\Core\Debugger\DebugInterface.h"
+#include "Common/CommonWindows.h"
+#include "Core/Debugger/DebugInterface.h"
 
 extern HMENU g_hPopupMenus;
 
diff --git a/Windows/Debugger/Debugger_Disasm.cpp b/Windows/Debugger/Debugger_Disasm.cpp
index 848a426e59..5e20f4a286 100644
--- a/Windows/Debugger/Debugger_Disasm.cpp
+++ b/Windows/Debugger/Debugger_Disasm.cpp
@@ -2,34 +2,34 @@
 
 #include "Core/Config.h"
 #include "Core/MemMap.h"
-#include "../Resource.h"
-#include "../InputBox.h"
+#include "Windows/Resource.h"
+#include "Windows/InputBox.h"
 
-#include "../../Core/Debugger/Breakpoints.h"
-#include "../../Core/Debugger/SymbolMap.h"
-#include "Debugger_MemoryDlg.h"
-#include "Debugger_Disasm.h"
-#include "Debugger_VFPUDlg.h"
-#include "DebuggerShared.h"
-#include "BreakpointWindow.h"
+#include "Core/Debugger/Breakpoints.h"
+#include "Core/Debugger/SymbolMap.h"
+#include "Windows/Debugger/Debugger_MemoryDlg.h"
+#include "Windows/Debugger/Debugger_Disasm.h"
+#include "Windows/Debugger/Debugger_VFPUDlg.h"
+#include "Windows/Debugger/DebuggerShared.h"
+#include "Windows/Debugger/BreakpointWindow.h"
 
-#include "../main.h"
-#include "CtrlRegisterList.h"
-#include "CtrlMemView.h"
-#include "Debugger_Lists.h"
+#include "Windows/main.h"
+#include "Windows/Debugger/CtrlRegisterList.h"
+#include "Windows/Debugger/CtrlMemView.h"
+#include "Windows/Debugger/Debugger_Lists.h"
 
-#include "../../Core/Core.h"
-#include "../../Core/CPU.h"
-#include "../../Core/HLE/HLE.h"
-#include "../../Core/CoreTiming.h"
+#include "Core/Core.h"
+#include "Core/CPU.h"
+#include "Core/HLE/HLE.h"
+#include "Core/CoreTiming.h"
 
 #include "base/stringutil.h"
 
 #ifdef THEMES
-#include "../XPTheme.h"
+#include "Windows/XPTheme.h"
 #endif
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 #include <windowsx.h>
 #include <commctrl.h>
 
diff --git a/Windows/Debugger/Debugger_Disasm.h b/Windows/Debugger/Debugger_Disasm.h
index bafd8d113e..41184baee7 100644
--- a/Windows/Debugger/Debugger_Disasm.h
+++ b/Windows/Debugger/Debugger_Disasm.h
@@ -3,17 +3,17 @@
 #ifndef _DISASM_H
 #define _DISASM_H
 
-#include "../W32Util/DialogManager.h"
-#include "CtrlDisasmView.h"
-#include "Debugger_Lists.h"
-#include "CPURegsInterface.h"
+#include "Windows/W32Util/DialogManager.h"
+#include "Windows/Debugger/CtrlDisasmView.h"
+#include "Windows/Debugger/Debugger_Lists.h"
+#include "Windows/Debugger/CPURegsInterface.h"
 #include "Globals.h"
 #include "Core/CPU.h"
 #include "Core/MIPS/MIPSDebugInterface.h"
 #include "Core/Debugger/Breakpoints.h"
 #include <vector>
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 
 class CDisasm : public Dialog
 {
diff --git a/Windows/Debugger/Debugger_Lists.cpp b/Windows/Debugger/Debugger_Lists.cpp
index 229cc71e6d..7efaac21a2 100644
--- a/Windows/Debugger/Debugger_Lists.cpp
+++ b/Windows/Debugger/Debugger_Lists.cpp
@@ -1,11 +1,11 @@
-#include "Debugger_Lists.h"
-#include <Windows.h>
+#include "Windows/Debugger/Debugger_Lists.h"
+#include "Common/CommonWindows.h"
 #include <windowsx.h>
 #include <commctrl.h>
-#include "DebuggerShared.h"
-#include "CtrlDisAsmView.h"
+#include "Windows/Debugger/DebuggerShared.h"
+#include "Windows/Debugger/CtrlDisAsmView.h"
 #include "Windows/resource.h"
-#include "../main.h"
+#include "Windows/main.h"
 
 typedef struct
 {
diff --git a/Windows/Debugger/Debugger_MemoryDlg.h b/Windows/Debugger/Debugger_MemoryDlg.h
index 764e8bbd3e..d324b50145 100644
--- a/Windows/Debugger/Debugger_MemoryDlg.h
+++ b/Windows/Debugger/Debugger_MemoryDlg.h
@@ -1,14 +1,14 @@
 // NOTE: Apologies for the quality of this code, this is really from pre-opensource Dolphin - that is, 2003.
 
 #pragma once
-#include "../W32Util/DialogManager.h"
+#include "Windows/W32Util/DialogManager.h"
 
-#include "../../Core/MemMap.h"
-#include "../../Core/CPU.h"
+#include "Core/MemMap.h"
+#include "Core/CPU.h"
 
-#include "../../Core/Debugger/DebugInterface.h"
+#include "Core/Debugger/DebugInterface.h"
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 
 class CMemoryDlg : public Dialog
 {
diff --git a/Windows/Debugger/Debugger_VFPUDlg.cpp b/Windows/Debugger/Debugger_VFPUDlg.cpp
index 4e25eff3f3..1d450145c9 100644
--- a/Windows/Debugger/Debugger_VFPUDlg.cpp
+++ b/Windows/Debugger/Debugger_VFPUDlg.cpp
@@ -1,16 +1,16 @@
 // NOTE: Apologies for the quality of this code, this is really from pre-opensource Dolphin - that is, 2003.
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 #include <windowsx.h>
 #include <commctrl.h>
-#include "..\resource.h"
+#include "Windows/resource.h"
 
-#include "../../Core/Debugger/SymbolMap.h"
-#include "Debugger_VFPUDlg.h"
+#include "Core/Debugger/SymbolMap.h"
+#include "Windows/Debugger/Debugger_VFPUDlg.h"
 
-#include "CtrlMemView.h"
+#include "Windows/Debugger/CtrlMemView.h"
 
-#include "../../Core/MIPS/MIPS.h" //	BAD
+#include "Core/MIPS/MIPS.h" //	BAD
 
 CVFPUDlg *vfpudlg;
 
diff --git a/Windows/Globals.cpp b/Windows/Globals.cpp
index 7c0016385b..1344fc94f4 100644
--- a/Windows/Globals.cpp
+++ b/Windows/Globals.cpp
@@ -20,7 +20,7 @@
 #include "MsgHandler.h"
 
 #ifdef _WIN32
-#include <windows.h>
+#include "Common/CommonWindows.h"
 
 // Globals
 HMENU g_hPopupMenus;
diff --git a/Windows/InputBox.cpp b/Windows/InputBox.cpp
index 2c8a753edd..cb19462ab9 100644
--- a/Windows/InputBox.cpp
+++ b/Windows/InputBox.cpp
@@ -1,6 +1,6 @@
-#include <windows.h>
-#include "InputBox.h"
-#include "Resource.h"
+#include "Common/CommonWindows.h"
+#include "Windows/InputBox.h"
+#include "Windows/resource.h"
 
 static TCHAR textBoxContents[256];
 static TCHAR out[256];
diff --git a/Windows/InputBox.h b/Windows/InputBox.h
index e75a0c95c5..75a939a108 100644
--- a/Windows/InputBox.h
+++ b/Windows/InputBox.h
@@ -1,8 +1,8 @@
 #pragma once
 
-#include "../Globals.h"
+#include "Globals.h"
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 
 bool InputBox_GetString(HINSTANCE hInst, HWND hParent, TCHAR *title, TCHAR *defaultvalue, TCHAR *outvalue);
 bool InputBox_GetHex(HINSTANCE hInst, HWND hParent, TCHAR *title, u32 defaultvalue, u32 &outvalue);
diff --git a/Windows/OpenGLBase.cpp b/Windows/OpenGLBase.cpp
index a0e7bf567c..c484cac566 100644
--- a/Windows/OpenGLBase.cpp
+++ b/Windows/OpenGLBase.cpp
@@ -1,12 +1,12 @@
 // NOTE: Apologies for the quality of this code, this is really from pre-opensource Dolphin - that is, 2003.
 
-#include <windows.h>
-#include "../native/gfx_es2/gl_state.h"
-#include "../native/gfx/gl_common.h"
+#include "Common/CommonWindows.h"
+#include "native/gfx_es2/gl_state.h"
+#include "native/gfx/gl_common.h"
 #include "GL/gl.h"
 #include "GL/wglew.h"
 
-#include "OpenGLBase.h"
+#include "Windows/OpenGLBase.h"
 
 static HDC hDC;     // Private GDI Device Context
 static HGLRC hRC;   // Permanent Rendering Context
diff --git a/Windows/W32Util/DialogManager.cpp b/Windows/W32Util/DialogManager.cpp
index fcfe80505d..fe77d9a481 100644
--- a/Windows/W32Util/DialogManager.cpp
+++ b/Windows/W32Util/DialogManager.cpp
@@ -1,6 +1,6 @@
-#include <windows.h>
+#include "Common/CommonWindows.h"
 #include <vector>
-#include "DialogManager.h"
+#include "Windows/W32Util/DialogManager.h"
 
 
 Dialog::Dialog(LPCSTR res, HINSTANCE _hInstance, HWND _hParent) 
diff --git a/Windows/W32Util/DialogManager.h b/Windows/W32Util/DialogManager.h
index 7f698186bc..856747b489 100644
--- a/Windows/W32Util/DialogManager.h
+++ b/Windows/W32Util/DialogManager.h
@@ -1,6 +1,6 @@
 #pragma once
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 
 class Dialog
 {
diff --git a/Windows/W32Util/Misc.h b/Windows/W32Util/Misc.h
index b1934b7759..2a53936967 100644
--- a/Windows/W32Util/Misc.h
+++ b/Windows/W32Util/Misc.h
@@ -1,6 +1,6 @@
 #pragma once
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 
 namespace W32Util
 {
diff --git a/Windows/WndMainWindow.cpp b/Windows/WndMainWindow.cpp
index a56c61e121..0b4f51bf2e 100644
--- a/Windows/WndMainWindow.cpp
+++ b/Windows/WndMainWindow.cpp
@@ -1,6 +1,6 @@
 // NOTE: Apologies for the quality of this code, this is really from pre-opensource Dolphin - that is, 2003.
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 #include <tchar.h>
 
 #include <map>
diff --git a/Windows/WndMainWindow.h b/Windows/WndMainWindow.h
index d061ffe951..8e5a367f2a 100644
--- a/Windows/WndMainWindow.h
+++ b/Windows/WndMainWindow.h
@@ -1,6 +1,6 @@
 #pragma once
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 #include <string>
 
 #include "Core/System.h"
diff --git a/Windows/main.cpp b/Windows/main.cpp
index 94c049e65c..b16f1d83e8 100644
--- a/Windows/main.cpp
+++ b/Windows/main.cpp
@@ -15,7 +15,7 @@
 // Official git repository and contact information can be found at
 // https://github.com/hrydgard/ppsspp and http://www.ppsspp.org/.
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 
 void LaunchBrowser(const char *url)
 {
@@ -25,14 +25,14 @@ void LaunchBrowser(const char *url)
 #include "file/vfs.h"
 #include "file/zip_read.h"
 
-#include "../Core/Config.h"
-#include "../Core/SaveState.h"
-#include "EmuThread.h"
+#include "Core/Config.h"
+#include "Core/SaveState.h"
+#include "Windows/EmuThread.h"
 #include "ext/disarm.h"
 
-#include "LogManager.h"
-#include "ConsoleListener.h"
-#include "Thread.h"
+#include "Common/LogManager.h"
+#include "Common/ConsoleListener.h"
+#include "Common/Thread.h"
 
 #include "Commctrl.h"
 
diff --git a/Windows/main.h b/Windows/main.h
index c882f098ee..2467aef030 100644
--- a/Windows/main.h
+++ b/Windows/main.h
@@ -21,7 +21,7 @@
 #include "Debugger/Debugger_Disasm.h"
 #include "Debugger/Debugger_MemoryDlg.h"
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 
 #define MAX_CPUCOUNT 1
 
diff --git a/Windows/stdafx.h b/Windows/stdafx.h
index 30f5a12f98..a298debe6e 100644
--- a/Windows/stdafx.h
+++ b/Windows/stdafx.h
@@ -61,7 +61,7 @@
 
 #endif
 
-#include <windows.h>
+#include "Common/CommonWindows.h"
 #include <windowsx.h>
 #include <process.h>
 #include <tchar.h>
@@ -75,7 +75,7 @@
 #include <string>
 #include <fstream>
 
-#include "Log.h"
+#include "Common/Log.h"
 
 #define THEMES