How to prevent VLC from automatically resizing its window according to viewed content resolution?

It is really tricky to find the checkbox that needs to be un-checked, so you could go edit the rc file (but don't use notepad.exe to do so, as the file will not be formatted).

C:\Users\%USERNAME%\AppData\Roaming\VLC

--- vlcrc.default       2011-12-16 11:46:51.000000000 -0800
+++ vlcrc.noresize      2010-12-05 20:00:26.000000000 -0800
@@ -1088,7 +1088,7 @@
 #qt-maximized=101

 # Resize interface to the native video size (boolean)
-#qt-video-autoresize=1
+qt-video-autoresize=0

Here is where you find the option in the interface.

Select Tools ⇨ Preferences ⇨ Interface then uncheck the box Resize interface to video size.
Finally, restart VLC.

First choose the window size you like the VLC window to be.

Then hold down the Ctrl and close the window with the X icon.

When you reopen VLC, it should open the window in the same size you closed it.