If you are convinced that a two party system is best for the country, then the negative impact of 3rd party candidates is that they siphon votes off of one or both of the main candidates. For instance, 3rd party candidate Ross Perot took votes away from George H. W. Bush in 1992, leading to a victory for the Democratic candidate Bill Clinton.
Others might argue, however, that 3rd party candidates are good for national elections. They raise issues for debate that might not be raised if only the two major parties were running.