Im not completey sure, but i have given it thought in the past. The way i figure it is that the season rank is calculated by all stat categories in a typical yahoo public league settings.
Basically they are ranked like the rotisserie league is calculated. Each player is ranked per stat category, and by how many players there are in the league, and the more points the higher the rank.
For example say there are 200 players in the NBA and Player A leads the league in the points category, they get 200 points, and the next person gets 199 points. So on and so forth.
Thats why it seems that players who shoot a lot of 3's, get a lot of steals, and blocks seem always to be ranked pretty high because its not a very competitive category usually. Unlike points where everyone has some input into it.
Again though, thats just my theory.