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If you have not defined ServerAliases for the non-www ServerName entries or vice-versa, then the server will default to the first VirualHost it finds, as documented.
A 301 redirect from www to non-www or vice-versa is recommended. This prevents multiple 'versions' of your URL from being linked-to by other webmasters, solidifies your site's 'branding' under one domain or the other, and prevents your PageRank and/or linkpop from being 'diluted' across two different domains.
I said two different domains; The major search engines will 'figure out' that these two domains resolve to the same content eventually, but then you are deopending on their back-end processing to do so. IMHO, it's better to just tell them up-front, and not rely on them taking the time to canonocalize your domain for you. This will make your ranking less 'fragile' IMO.
The top sites you saw may be succeeding in spite of these canonicalization problems. Try entering google.com in your address bar, though. Google thinks it's important. Instead of checking the 600-pound gorillas in whatever market segment you investigated, take a look at the smaller up-and-coming sites below them. Those that seem to be performing above their potential may indeed have all their server-side details in place.
Note that above, I didn't use the word 'penalty.' Webmasters see penalties in every dark doorway, and in some cases, invent them to compensate for poor SEO, design, or usability of their sites. In that regard, a warning: Users generally don't like their time being wasted with 'splash pages.' And if your splash page is done in Flash, your site won't perform in search unless you also provide lots of text for search engines to chew on.
This can be done on the same page, or you can 'cloak' for search engines. If you do that, though, make absolutely sure that your non-Flash page is usable by humans, and that it contains absolutely the same content as delivered in Flash -- No more, no less. In this way it is cloaking, but cloaking with no intent to deceive. If you wish to pursue this subject further, I'd recommend getting a 'second opinion' in some of our other forums here -- I'm far more comfortable discussing Apache that SEO for splash pages... :)