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Thats easy... xoops.
I used phpnuke for 3 years before i discovered XOOPS and when i found xoops, it was like a hot knife through butter.
Because nuke has more people, it also has more crackers, so IMHO its a bigger security risk.
Nuke seems to be really run by one guy and whoever he deems worthy. But its not a truly open project, IMHO. Meanwhile, all phpnuke dot org has on it is a bunch of useless ads becuase he is trying to suck every dime out of it. And the new features have slowed dramatically. Sure it has alot of module developers, but most of them are really really bad.
Xoops is Object Oriented. Nuke is not. this is important when time goes by. its also easier to code in OO. So developers like me really love our work for xoops.
Flexibility? well XOOPS is the most flexible CMS I have run across thus far, and im no longer looking.
The update function updates a module after you upload any new files or make changes to the templates and config files, without screwing up your database.
Yes, the update feature is very well made. For users who do not code, I think its the greatest thing ive seen in a cms. Webmasters should really love how easy XOOPS is to administer.
Xoops is rad.
Cheers,
-Lavaburst