When I was using SymLinks, I had it set up like this:

Parent Folder --- > WoW A
--- > WoW B
--- > WoW C
--- > WoW D
--- > WoW E
--- > WoW F

The idea was to only ever patch the parent folder, and to not use that to play any toon with.

WoW A-E were my five box folders, with graphical options down to almost nothing.
The addons were slightly different, with WoW C (tank's account) having a few more then the others.

WoW F was my single box account, which at the time was a Warlock.
This folder had every single option cranked to the maximum.
Unlike the WoW A-E folders, I did not add -nosound to the end of this executable.

Different settings is the main benefit.
In the original SymLink thread, the consensus was a SymLink set up was faster then five folders or everything from one folder. In my case either this was not true, or the difference was too marginal to notice.

I had a bunch of issues patching twice.
One install works fine for me.
I miss some of the eye candy now, but run my raider (rogue) and boxing teams all at minimal settings.