The first PowerPC linux for the Power Mac ran under the Mach microkernel [1].
Then there was also L4Linux, which I believe was the first low-overhead virtualization of Linux using the L4 microkernel. Papers demonstrated < 10% overhead I believe, where previous virtualization efforts were somewhat higher. I'd say it kicked off the whole paravirtualization/virtualization craze.
http://www.yodaiken.com/papers/BarabanovThesis.pdf [1997]
Well, that's not exactly a microkernel, but took lots of inspiration from microkernels.
I take it that you may be alluding to the debate between Torvalds and Tannenbaum regarding microkernels.
https://en.wikipedia.org/wiki/Tanenbaum%E2%80%93Torvalds_deb...