I have five wow folders, \wow1 - \wow5. Wow1 is the only "real" install, all the rest are junction'd off \wow1. One thing I did was NOT junction the WTF folder, but instead the WTF\Account folder. That gives each Wow folder its own wtf\config.wtf, which lets me give each one different video, audio, etc settings and they stick.

The script I use (XP, not sure about Vista) to create extra wow dirs is pretty simple and copied from a script previously posted here:

Code:
 
@echo off 
set MYDIR=%1 
mkdir %MYDIR% 
FOR /f %%I IN ('dir /b /a:-d wow1') DO ( 
echo %%I 
fsutil hardlink create %MYDIR%\%%I wow1\%%I 
) 
junction %MYDIR%\Cache wow1\Cache 
junction %MYDIR%\Data wow1\Data 
junction %MYDIR%\Errors wow1\Errors 
junction %MYDIR%\Logs wow1\Logs 
junction %MYDIR%\Patches wow1\Patches 
junction %MYDIR%\Screenshots wow1\Screenshots 
junction %MYDIR%\Fonts wow1\Fonts 
mkdir WTF 
junction %MYDIR%\WTF\Account wow1\WTF\Account 
mkdir %MYDIR%\Interface 
mkdir %MYDIR%\Interface\AddOns 
junction %MYDIR%\Interface\AddOns wow1\Interface\AddOns
Run this from the root of the drive you are creating new wow's in (or change all the wow1\ to c:\wow1\ or whatever).

One thing to be extra careful for when doing this though is never, ever, ever delete a file inside any of the wow2, wow3, etc folders. it WILL delete the wow1 equivalent! I accidently deleted my Addons folder once and didn't realize it, fortunately I had made a backup the night before.