I have compiled a list of website links that have various fantasy football and other games that are different from the regular Draft and choose Lineup fantasy leagues. 

Some of these are from sites you are familiar with (for example NFL.com) but some are less known and from blogs. I included a bunch of free ones with prizes (and some that have small registration fee's for those that would like higher chances of getting prizes). Surprizingly there weren't many this year from big companies doing promotional games, like Best Buy or food companies, etc, but please post info if you are aware of others.

There are lots of links, but I'm sure some people here on Niners Nation will end up registering for as many games as they can :)
Hopefully some of us can create Niners Nation leagues from the sites that allow it and please post the info here so others can join it aswell. 
Good luck!

http://www.fsmfantasysports.com/ - pick player weekly but can only select a player once the entire season for the roster - Free and $20 fee option

Fooch posted the next one http://www.ninersnation.com/2010/8/31/1660191/johnsonville-rush-for-2000-yards#45679067 http://www.rushfor2000challenge.com/ - select running back

http://www.fantasysharks.com/artman2/publish/Contests_Now_Available_2010.htm - regular team pick-em, team pick-em elimination, and top player scorers contests
 
http://football.cbssports.com/splash/football/spln/opc - free regular team pick-em
I think CBSsports has some sponsorhip stuff with SBNation so go to this site for the fantasy league and get discount

http://football.fantasysports.yahoo.com/pickem - free regular team pick-em

http://msn.foxsports.com/fantasy/football/survivor/?e=0 - pick the team to win but can only pick a team once http://msn.foxsports.com/fantasy/football/pickem/ - regular team pickem each week

http://challengegames.nfl.com/landing/hometeamchallenge - pick weekly roster from each position - prizes based on favorite team selected http://fantasy.nflrush.com/rush/pages/how_to_play - only if you are under 15 years old, with prizes

http://games.espn.go.com/pigskin/en/frontpage - regular or against the spread weekly pick-em http://games.espn.go.com/eliminator/en/frontpage - pick-em one team each week and can only pick team once http://games.espn.go.com/gridiron/en/story?pageName=gridiron\prizes - free, with only 2 total prizes and no weekly prizes, manage a team with salary

http://lasvegas.profootball.upickem.net/profootball/registration/login.asp - pick-em contest

http://propicks.hgtvpro.com/ - pick-em

http://www.fftoday.com/contests/3andout.php - pick, QB, RB, and WR, same player only once - $13 fee

http://www.fanball.com/draftandplay/?ArenaID=1# - $10 fee draft league with small number of teams

http://www.suicidefantasyfootball.com/pages/suvivor-football-pool - entry as low as $10

http://fantasy911.com/Index.aspx?NFL - wide variety of low cost weekly games

Other links that I saw but have have not looked into

http://www.bankrollsports.com/blog/2010-free-ncaa-nfl-football-contests-list-updated-815/ http://www.cappersinfo.com/forums/http://www.sportsco.com/football/football.htm http://www.eatdrinkandsleepfootball.com/php/forums/forumdisplay.php?f=97