This means that Bomis' collection copyright would be violated if somebody were to copy the website wholesale. If on the other hand the wiki sources of the articles are downloaded one by one, and a new web site created out of those, then Bomis' collection copyright won't be violated. If this new web site doesn't offer the articles under GFDL, then the individual article authors could sue of course.

There's a little more to it than that: copyrights apply to "creative expression", and "selection" of what to present is a creative act specifically recognized (see Feist v. Rural). So it doesn't matter how they acquire the whole collection, whether they copy the website whole or download the articles one by one; if they present the same collection of articles that we do, they have violated our copyright on that creative choice of which articles to present.

This is similar to a Linux distribution. If you create a distribution, you can claim collection copyright, and somebody who copies the CDROM image without permission is in violation.

...that's true...

Everybody can however create their own distribution out of the exact same free software components that you used, without violating your collection copyright.

...but that's not true. You /can/ be sued for violating a collection copyright for publishing the same collection of free components as someone else, regardless of how you acquired them, and even if you package them differently. Choice of what to present is a creative act, and is protected. 0