R. Belmont already suggested this, but I also want to recommend IDA Pro + emulator debugger as a great combination to study what the program is actually doing.
Unfortunately, I believe that the free version only will disassemble x86 (last I checked) so I recently (earlier this year) shelled out something like $600 for the "starter" version which is way more than I need but after getting over the initial price pain, I am quite pleased to have it in my toolkit.
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Re: Debugging 6809 RAM writes with MAME debugger (Robotron 2084)
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