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You can at least debug the windows kernel using IDA+GDB (if you enable the GDB debugging interface in VMWare, for instance). I haven't tried the same for Linux or QEMU, but I think it should work. You can even set the resp. options to debug real mode code in the debugger specific settings of the GDB module.
This might help:
http://www.hex-rays.com/products/ida/support/tutorials/debugging_gdb_windows_vmware.pdf
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