Take a look at HelenOS, which is a from scratch microkernel based OS that aims to be a fully modern OS. Disclamer, I'm a contributor, I'm working on its shell from scratch.
HelenOS has been ported to ia32/64, SPARC, ARM and more, its very well designed and easy to read. Its still in its infancy but shows one possible design that really takes advantage of the microkernel design and solves many issues in a microkernel implementation (such as IPC).
It also includes scripts that automatically set up a proper tool chain needed for cross compiling. Its very easy to build and runs very well in most simulators (i.e. QEMU) or bare metal.
I would also study L4, Minix3 and the GNU HURD (based on Mach), the latter being an illustration of design pitfalls when trying to leverage a microkernel.
If you want to go the monolithic route, just study Linux.
