I got this running on qemu by cannibalizing a tiny bit of code from xv6 (http://pdos.csail.mit.edu/6.828/2012/xv6.html) to replace the GRUB dependency. After cloning and building mkernel according to its instructions:

  $ git clone git://pdos.csail.mit.edu/xv6/xv6.git
  $ cd xv6
  $ make

Now you should be able to run xv6 by itself:

  $ path-to-qemu/x86_64-softmmu/qemu-system-x86_64 -serial mon:stdio -hdb fs.img xv6.img -m 512

To run mkernel on qemu, we'll replace xv6's kernel with mkernel's:

  $ dd if=/dev/zero of=mkernel.img count=10000
  $ dd if=bootblock of=mkernel.img conv=notrunc
  $ dd if=../mkernel/kernel of=mkernel.img seek=1 conv=notrunc

Now you can boot up the mkernel.img rather than xv6.img:

  $ path-to-qemu/x86_64-softmmu/qemu-system-x86_64 -serial mon:stdio -hdb fs.img mkernel.img -m 512

(Based on xv6 at hash ff2783442ea2801a4bf6c76f198f36a6e985e7dd and mkernel at hash 42fd4c83fe47933b3e0d1b54f761a323f8350904. Ping me if you have questions; email in profile.)