"In one study participants thought that their sarcasm would be communicated 80% of the time. Face-to-face this was accurate, but over email the actual figure was 56%.
This overconfidence was also seen when people tried to communicate anger, sadness, seriousness and humour in an email. Without body language cues, it's hard to communicate more than literal meanings."
While emoticons are fun and can be helpful, they do not convey the breadth of emotion we convey in our body and facial language. If you must criticize, complain, or negotiate, try to get a face to face meeting with the other party. If that's not possible, at least use the phone where tone of voice cues help convey emotion. As a last resort, try a visual email tool, such as eyejot.