Is yoga an acceptable form of meditation for a practicing Buddhist? Yoga is a form of mediation which involves physical exertions as well as inward examination.  Is this an acceptable form of meditation for a Buddhist?  Are there any sects of Buddhism which focus on meditations which involve physical exertion?
It depends on what your definition of 'acceptable' is.  Will it benefit you?  Absolutely.  For one, a case can be made that yoga is a mindfulness-of-the-body meditation and that it can even go beyond that - incorporating other aspects of sati (mindfulness).  I think it's also safe to say that all five of the hindrances can be temporarily suppressed during intense yoga and may even give rise to access concentration (upacarasamadhi).

Still, I don't think it's a perfect substitute for the kind of meditation the Buddha taught.  For starters, I wonder whether true jhana is available to someone in an asana other than a variant of the lotus position.  You'll be able to attain some amount of samatha, but the degree will be lessened by the effort it takes to maintain the other asanas.  Outside of lotus, I also don't think you'd be very stable, physically speaking, and that you'd probably just wind up falling over!  But maybe you aren't even looking to attain jhana.  Who knows!  There is precedent that such states aren't a prerequisite to enlightenment.

As per 'sects' of Buddhism that use physical excursion, well, there is a rich tradition of doing prostrations, schools like Tendai have their mudras (but I'm guessing that's not the kind of exertion you're talking about), and many martial arts schools with a Zen slant pay strict attention to bodily position - especially Japanese styles like iaido (and come on - meditate with a sword?  How cool is that!).

So yes - beneficial, absolutely.  A true alternative?  Mmmm...probably not.