That discussion about Webmin and Ubuntu/Debian configuration files has been inaccurate for
years. Within a few weeks of the problem being known, it was corrected, and Webmin is quite respectable of the Debian way of dealing with configuration files (the specific case was Apache configuration files, if I recall correctly, but the firewall module supports the interesting Debian layout, and the init/rc handling modules were updated to deal with the rc system in the way the Debian developers requested), and no one involved in Webmin development has ever expressed any reluctance to do things "the right way" on Debian or any other OS. If someone reports a bug, the problem gets corrected, usually in the next release of Webmin. In this case, no one reported a bug, and so it didn't get fixed for a while (Jamie didn't use Debian or Ubuntu at the time, and so was reliant on others to report problems...though we both have Ubuntu and Debian development boxes today).
I'm not sure why Webmin hasn't found its way back into Debian or Ubuntu, since the problems were corrected promptly once they were reported upstream. Somehow it became a highly politicized issue for a few people (I suppose the people who were working on eBox), and I washed my hands of the whole discussion. There are a few (like two or three) developers who loudly, angrily, and aggressively, oppose Webmins inclusion for seemingly personal reasons, and Jamie and I don't have any desire to argue with them about it.
Jamie maintains .deb format packages available at Webmin.com, and I maintain apt-get repositories for Ubuntu 8.04 and Debian 4.0 at Virtualmin.com (which also includes all of the Virtualmin packages and dependencies).
eBox, as far as I know, has only a dozen or so modules (vs. 114 standard modules in Webmin and a couple hundred 3rd party modules), and is still several years away from being a reasonable replacement for Webmin (if that is, in fact, their goal with eBox).
I would encourage you to look at both, if you aren't sure which tool is appropriate for you. And if you're using it for virtual hosting tasks, as seems like, since you're asking here at Linode, you might also wish to try Virtualmin--it's also free and Open Source, though there is a commercial version as well. Usermin is also a pretty nice webmail client, though it still needs some UI work.
Feel free to ask questions on the Webmin mailing list, the Virtualmin.com forums, or even here (I don't follow the forums here very closely, though...so you might ping me directly if you have something here you'd like me to look at). And there's an extensive wiki here, covering nearly all of the modules in quite good detail:
http://doxfer.com/Webmin
Hope this helps with your plans.
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