Haha well I guess there will always be non-believers. Don't worry though, when I get this uber auto debugger working I won't hold any grudges against those who doubted.

KingMike, those situations shouldn't be a problem as the system would effectively go through all situations possible. I'm not sure about BoF2 by Shining Force 2 has a point where you have to select between 4 characters so at this point the system would select the first one and record the way it branched and continue on then at a later point it would return and make the other choice and so on and so on.
FinS, yeah I think you're right with the way of using it and you're definitely right with the need to reinsert the data. This of course assumes we can't get an automated version working instead.
Well Nightcrawler I guess after making it I would just print it out and hang on my wall cause it would be pretty cool to have a full disassembly of a game hanging on my wall

Other people might find better uses for it but that would be up to them. Have any interesting things been done with any of the full disassemblies out there? (I know this wouldn't produce fully commented, ordered or anything near those ones)