Title says it all. If it's not done by simply flagging certain commands how is it done?
"Most" of the console commands in game will mark you as a suspicious player as confirmed by Adam Perin from Runic. There doesn't appear to be a more specific list available.
In addition, if you have been flagged, it is not apparent to you - only to other players you're playing with online. In the instance you have been flagged, your characters' name plate will be preceded by a red !.
A full list of console commands can be found here.