Chakotay/Seven - Came from absolutely nowhere right at the end of the series, it was more of a distraction than anything else in the finale with them trying to put some sort of relevance on a relationship that the audience was not invested in at all.
Michael/Jan from The Office - This was ok until they turned Jan from a professional business woman into a complete nutjob. It would have been more interesting to have her keep her job and try to juggle the relationship with a guy she had to manage.
Rodney McKay/Jennifer Keller from Stargate Atlantis - I liked the Katie Brown/Rodney relationship better. There was more chemestry between them.