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For me, I find that XOOPS fits my needs better than phpNuke did. I have no vested interest in any particular CMS. I only run small game/personal interest sites. Your needs might require something different. For me, the biggest differences between XOOPS and phpNuke are modules, themes and updates. I've run Nuke for several years and have been switching those sites over to XOOPS these last few months.
phpNuke has a LOT of modules for a huge variety of things. On the surface that's a good thing and I miss it. But there doesn't seem to be any interaction between mod developers in phpNuke. Whenever I installed a phpNuke module I was rolling the dice as to whether my admin menus would work anymore. In Xoops, I have never had this issue. Due in large part to the Module Dev Forge and strong community discussing matters on the development site here instead of on multiple fan sites with divergent agendas is a really nice thing.
Themes seem to be easier to modify in Xoops. But that is likely just be my knowledge of css, xhtml and php have improved over the years. I do however like that there are a number of people working towards tableless themes and actively considering standards. I need to learn more about Smarty to see whether it will be useful to me.
Updates are painless and timely. In phpNuke, since the fixes to the core code went to Francisco's paid users for a few weeks before public release, it took some time.... This was particularly frustrating in light of the increase in defacement and sql injection attacks last year. XOOPS is very secure against those issues as far as I can tell. Truth be told, I haven't seen a single compromised machine due to XOOPS since this spring when I started looking at it.
Well-coordinated, easy to integrate with straightforward installation and administration. XOOPS works.