Shipping wars result when tensions arise between fans (or Shippers of two (or more) different character relationships (or 'ships) in either canon or fan fic. The fiercest wars occur between adherents to different OTPs.
There was a noted absence of shipping wars in the first four seasons, due to the presence of only two main characters - Sam/Dean - if a fan was comfortable with Wincest. The main wars, which are ongoing, were mainly between Sam Girls and Dean Girls.
The emergence of Dean/Castiel as a popular 'ship in 2009, has resulted in ongoing skirmishes and battles between supporters of Destiel and Wincest over whether the relationships are supported by canon, and which one is the true OTP in a classic example of Shipping wars. Blood has been spilled in this war.
Tensions can arise anywhere. The Supernatural Newsletter divides fanfiction into categories - Dean/Sam, Other Slash, Het, Gen and RPS and Other (mainly crossovers). Dean/Castiel fic is included in "other slash", however some fans of the OTP felt it deserved its own category. In October 2009, the Dean/Castiel newsletter was created. In January 2010, the community SamDean OTP started its own weekly newsletter for fanworks featuring only Wincest. An number of other pairing specific communities have arisen since.
In RPF, Jsquared is the OTP for most and so shipping wars are almost non-existent, although both actors occur in a number of pairings both Slash and Het. Surprise JDM is considered particularly disruptive to the OTP.
- This entry on Fandom_Wank illustrates the intensity of shipping wars in the otherwise benign fandom related to the TV show "Chuck".