Wow, I can talk about mods without fear of being banned from the forums! Of course we already did tinker with the game files, like the buildings-off utility in Caesar III, but only mentioned such things as a side remark at most. There are several such utilities for C-III, I also have some for Pharaoh, but I'm not aware of any for Zeus or Emperor. The link that Gweilo gives above to the miscellaneous section of the download central does not seem to contain the items he mentions.
For Emperor there is the point that you can play it in multiplayer mode, in which case of course a modified version of the game can easily involve cheating of the kind that could go undetected. As long as you play single player mode only, that problem does not arise.
At CBC we recently have had a problem with modified game files in Children of the Nile. In a beauty contest players had used graphical mods, which were freely available at the TM-forums BTW. Since those mods didn't show up in the cities assessed by the judges, judging was at an equal base, but other modifications than graphical made for an unlevel playing field. Also for contest play you need the original game unmodified files, or decide beforehand what mods are accepted.
The Code of Conduct of course is written to prevent discussions leading to p.i.r.a.c.y. That of course is a no go area, but maybe the CoC needs rephrasing. Rules are needed to restrict illegal behaviour, but if those rules mainly have the effect of actually restricting harmless fun, then by all means mod the rules.
Mods: Please feel free to mod my post if you think I'm crossing lines.