Let's discuss how to set up a scoring system for your games. The best thing to do in selecting a scoring system is to make sure all the owners in the league understand the system, and that it approximates their level of NFL knowledge. Outside of that recommendation I suggest that leagues try bonus scoring with individual defense. That means players score points for their yardage, touchdowns, and get a bonus if they pass a certain yardage threshold. Defensive players are drafted and get points for tackles, sacks, interceptions and fumble recoveries.
Whatever the scoring method, try to avoid complicating it too much. Don't change point values if different positions do the same thing. For example, a passing touchdown shouldn't be worth more for a wide receiver than a quarterback. Don't make use of silly stats like yards per attempt, distance of score(unless it's a field goal), or numbers of attempts. Don't penalize NFL players by subtracting points either.
While I can see the argument, "if it hurts an NFL team, it should hurt the fantasy team too," the other side can be looked at as well. Fantasy teams are made up by players who probably don't play together in the NFL. Your fantasy quarterback shouldn't be penalized if an interception occurs when his NFL receiver falls down. Also, subtracting points adds complexities to your scoring system without adding to fantasy enjoyment.
Finally, try to balance your scoring system so that the player values are like the NFL. Quarterbacks and running backs have the most value, followed by receivers. Linebackers are the most valuable defensive players, followed by top defensive backs and linemen. Kickers are a dime a dozen. So, go set up your league and have fun.
I will use this scoring system if I am discussing players: Passing TD 4 points, Rushing/ Receiving/ Defensive TD 6 points, 10 yards Rushing/ Receiving 1 point, 20 yards Passing 1 point, Over 100 yards Rushing/ Receiving 3 bonus points, Over 300 yards Passing 3 bonus points, Tackle 1 point, Sack 4 points, Interception 5 points, Field Goal 3 points, Extra Point 1 point.