Outside of the normal negative points, I have used the following system for many years and it balances out fairly nice.
TDs - 6 for rushing/receiving and 4 for passing
Yards - 1 for 10 rushing/receiving and 1 for 20 passing
1 point per reception for everyone but RB's. RB's get .5 per reception.
Of course every year you will have anomolies, but for the most part, this keeps many of the positions in line with each other. And to spice it up a bit, we give bonus points for long TDs of over 40 yards. Nothing more than that, just a bonus at TD scored of plus 40. Since these big plays don't happen all that often they don't normally determine a game, but it does make things a little more interesting.
My Playoff Team - Please Comment
MSchaub, DMcNabb, JFreeman, KKolb
SJackson, THightower, CWells, JForsett, JSnelling, CJennings, QGanther
RWayne, RMoss, RMeachem, MCrabtree, DBowe