Hmm... I just tried to run Oenology through the service, but someone had already done so. It only got a 99. :/

It seems that the site has escalated the severity of an INFO check (use of include()/require()) to the level of a warning. The end result is that a legitimate (and proper) use of include()/require() - to include functional files in functions.php - causes the rating to be downgraded.

So, there's some room for improvement there. But, in all fairness, there's room for improvement in that check in the Theme Check Plugin as well. That INFO output should only be given if include() or require() are used in template files. The use of include() and require() should be ignored when used in functional files. So, that's not entirely the fault of the themecheck.org site (though I'm unsure why an INFO check is being escalated in severity).