ideas (some of which have already been mentioned)
Change the draft order, so there is an incentive to not finish in the bottom. For instance, Have the draft order go (based on last year's standings (7-12, 6-1), so the worst team doesn't really get a great pick the next year.
If you do not reach a minimum number of innings, you get no points in any pitching category. This is most valuable if you adopt the reverse drafting mentioned above.
Have the last team (or two teams) lose a keeper. If you get 10 keepers, you may have people punting their entire season to get 10 great keepers. Well, make it so if someone doesn't finish above a certain level they lose a keeper. So anyone who finishes below 35 points, only gets to keep 9 players. Anyone who finishes below 25 keeps 8, anyone finishing below 20, keeps 5 players. If the benefit of punting is great keepers, then optimum punishment will be the complete opposite.
Last place team (or team that loses the most points in the second half) gives $100 to the team with the most improved record in the second half