It occurred to me during the Megillah reading that we only make noise and "stamp out" Haman's name when he is referred to as "Haman." Why don't we "stamp out" the name of Memuchan, who the Sages tell us was actually Haman? For that matter, why don't we do the same during other Torah reading when any bad guy, Amalek for instance, is mentioned?
Good question! The answer may be that although Memuchan refers to Haman, it is not his actual name. Part of the original custom to "stamp out Haman's name" was to say "shem reshaim yirkav - may the name of evil people be erased."
Now for your second question, why don't we "stamp out" the name of Amalek and other "bad guys?" The truth is, it's not really appropriate to make noise during the Torah reading in the first place, but it's permitted during the Megillah reading because of the special joy of the day. There are in fact authorities who discourage it even during the Megillah reading, and they only allow it because it is already an established custom.
Also, it is only appropriate to make noise when referring to a story in which we emerged as the clear winner, and with Amalek, that has not yet happened.