I think your instinct is right Blake, avoid adding .html/.htm to the PHP Engine if not absolutely necessary. PHP documentation slightly touches on the fact this could have a performance impact, but doesn't get into a lot of detail... in an article talking about hiding PHP from attackers/visitors.
See PHP Documentation: Hiding PHP
Your question, based on the subject line of this thread is deduced as, [Are there] includes that work in HTML and PHP in IIS 7 on Windows Server 2008 [?].
If you already have SSI enabled on IIS, then doesn't this already work in PHP as regular html, the way you have been doing it? Or are you looking for yet a 3rd include option that isn't SSI module or PHP engine/include function that works in both HTML and PHP code? If SSI does what you want, and you already have that loaded on your Windows server and have dedicated time and resources developing and securing it, AND it works with PHP, why look for another option? I don't mean this to be confrontational, just trying to learn a little bit more about the problem you are trying to solve.
Otherwise this works just the same:
echo "<!--#INCLUDE file=\"/includes/header.inc\"-->\n";