Bitminter pays minimum fees on auto cash out transactions. This has usually worked well, but right now there appears to be a big boom in bitcoin usage.
The number of unconfirmed transactions is very high and growing rapidly. I've changed our settings to make bigger blocks and include more free and minimum fee transactions. Hopefully that will help somewhat, but I think we need other pools to do the same.
Maybe you could set a higher payout threshold where if you get your payouts at that threshold, a fee is paid? Looking at some of those hung transactions, there are some fairly hefty payouts waiting a long time. I seem to have been extremely lucky that my meager payouts happen to have gone into bulky blocks that had a fee paid.
Or perhaps you could let people click a flag that they are optionally willing to contribute to a fee - then when payouts are made, fees are distributed evenly among those who clicked the fee checkbox. This would probably result in some free riders, but it would at least give people some chance to influence the payout to confirm quicker.