Shipping wars result when tensions arise between fans or shippers of two (or more) different character relationships (or 'ships) in either canon or fanfic. 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 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.
For other related terms see:
In RPF, Jsquared is the prominent ship, with many of its shippers engaging in Tin hat speculation regarding Jared and Jensen, with behavior that often mirrors the behavior of shipping wars. Cockles is a fast-growing RPF OTP rival along with Mishalecki. These other pairings and are considered disruptive to the Jsquared ship. Surprise JDM is disruptive to all other OTPs.
All of Supernatural's actors occur in a number of pairings both Slash and Het, but the overlapping RPF and Fanfiction ships of many fans means the battle lines of the shipping wars are at times muddied.
- This entry on Fandom_Wank illustrates the intensity of shipping wars in the otherwise benign fandom related to the TV show Chuck.