Ive heard allot of bad stuff about this mod, but i have yet to get a problem with it. I think its a good way to update your addons.
Basicly, im just wondering if its bad using it :P If not, you can grab it here (http://wowus.m6.net/) :)
The thought about a program that automates all the work with updating all the add-ons does indeed sound very tempting. I read briefly through that site you linked, and features such as automatic backup of the old add-on versions, saved variables etc will be very handy indeed!
The only potential "bad" thing I can think of, is that I'm not sure I would trust any other programs than one made by Blizzard to automatically add and remove things in my WoW folder. This is of course based on all the horror stories we have heard about key-logger programs etc. used to steal people's account information.
Now I can say that I haven't heard of anyone that have had their account hacked from using such a program, and I would also guess that the word would spread pretty fast if it had happen, but still, I wouldn't feel all comfortable with it.
I also noticed that it didn't have PhotekUI (which I have tested for a week now, and I love it :D) on that list... but than agian, PhotekUI ain't one add-on, but a compilation of many addons (which most of 'em I found on the list), so I could simply just add all the add-ons that Photek include... But that would again give me quite some work when Photek add/remove add-ons from their list...
Just add all the addons you have in a compilation and dont want to update in the execlution list, and they will be ignored by wowus :) Genious :P