Hi!
They do. Google ditched all existing database and built their own system to handle their main stock and trade. For some things, they use MySQL, albeit a modified one.
Their main stock of trade is selling ads, and even though nobody will ever admit what they are running in publicly, MySQL Conference few times had engineers from ads that were very familiar with MySQL internals and did talk about large scale enterprise deployments. :) By the way, we are running same patches they were running at some point in time. There's a joke though, about our 'four oh forever' build :-)
Yahoo uses PostgreSQL (again, a heavily modified one): http://www.informationweek.co/news/showArticle.jhtml?articleID=207801579
Is it web facing, or a data warehouse? Yahoo is quite federated environment, but it also has swarms of MySQL engineers there. Some of properties were running stock distribution packages, though... :)
Keep in mind if popularity alone was a good criteria, we'd all be <strike>happily</strike> using Windows on our desktops. If all that mattered was technical superiority, we'd be running BeOS. :)
Ease of use is an important component, when you need to build large scale-out infrastructure. Software products end up being building blocks instead of central nerve pieces, and individually shouldn't need too much attention.
Frankly, the choice of using PHP as the language for MediaWiki has probably caused more problems over the years than the choice of database backend. :)
:-) Choice of database backend didn't cause lots of problems over last years, did it? OTOH, PHP worked quite well in this opensource mediawiki project, I'm not sure which other language would've got more/better quality contributions. Erlang maybe? :-))
Domas