Problem #1: if there were a plausible reason why a particular NPC would 1) know who I am and 2) know what I have done, then systems like these might make sense. But I've never seen such a system yet. Typically, NPCs all over a game world appear to have access to a database containing accounts of every action I have taken. NPCs I have never met psychically know of my deeds. These systems need to be more sophisticated than what we have seen so far.
Problem #2: assuming, hypothetically, that a system could be crafted that did make sense, the system needs to serve a valid roleplaying purpose. There needs to be a reason why I should care what my reputation or Karma is. There should be serious repercussions to my actions. Some actions should block my progress in certain areas of the game later on. Some NPCs should stop talking to me, or even turn hostile. At extreme levels of Karma or reputation whole towns or regions of the game should become off-limits. Some quests (outside of the main quest, possibly) should be rendered unavailable.
If a Karma or reputation system only gets us better prices with merchants or controls which companions we can travel with, it is little more than a gimmick, in my opinion, and should not even be in a serious roleplaying game.