A Keeper league in Fantasy Football refers to a particular type of league where one chooses to retain select players from season to season.
There are many variations of keeper leagues and many formats. Typically the standard keeper league allows each owner to retain one, two or three players on their roster to "keep" for the next NFL season. Keeper leagues can also include other variants such as you can only keep a player one time- Say owner "A" has Peyton Manning, Owner "A" decides to keep him for 2008 thus will not be eligible to keep him for 2009.
After each team has chosen his or her keeper(s) a standard draft is held. Variations to keeper leagues primarily just include the number of players you are allowed to keep and rules regarding previous "kept" players.
Keeper leagues add a bit of an interesting flair to fantasy play over your standard redraft league. Keeper leagues give a more sense of continuity between seasons and offer a more strategic element that is not found in standard redraft leagues.