They're two different Mixed Martial Arts organizations. However, both are owned by the same parent company, Zuffa. And to the idiot who said Miguel Torres should fight in the UFC, your an idiot, Torres fights at 135 pounds, its called the Bantamweight division. The UFC goes from heavyweight (265 lbs) to lightweight (155 lbs). Although I believe Torres has fought once at lightweight but 135 is his natural weight class.
The WEC is owned by the UFC and is all in the same group of mix martial arts. The WEC focuses on lighter weight classes and the UFC you will see more of the middleweight, light heavy, and heavy.
Both UFC and WEC are owned by Zuffa.
WEC was meant to be for the lighter weight classes, hence the presense of Featherweight and Bantamweight in there.
WEC also being used by Zuffa to put fighter from UFC that is deemed exciting but has had string of losses in UFC (ie. Scott Smith or Jens Pulver) or if they want to change weight class.
As for the other answerer, Affliction is formed by M-1 global along with Affliction clothing owner, with experienced people like Big John McCarthy and Randy Couture involved in it. One of the money backer for Affliction is actually Donald Trump himself.
By all means, Affliction is not a minor league since they have some of the best Heavyweight in the world. Something that UFC always lack.
The difference is in weight division and stars for the most part. When the UFC was expanding its league, it got to the point where it made sense to have two leagues and have one concentrate on smaller fighters by the pound. WEC started from SuperHeavyweights to Bamtamweights, but now it concentrates on Lightweights to Bamtamweights and is soon adding a Flyweight division. This means it only features 155 lb. fighters and anyone else lower in weight. The UFC has for years now featured almost only fighters between 155 and 265. So you won't see stars like Miguel Torres and Urijah Faber on UFC, they are in the WEC, which is a basically a spinoff league still connected heavily to Zuffa and the UFC. We may even see a women's league one day in the UFC, or more likely, the WEC since it concentrates on lower weights.