Application Fee Structure

My mid-size [Iowa] city (pop. 70,000) is revising our current fee structure. We want to capture a greater share of the costs associated with processing applications (things like subdivisions, Planned Area Developments, Rezonings, Variances, Special Exceptions, etc.). Most likely, this will include some evaluation of staff time which most Iowa cities haven't actually determined, though we probably don't want to be too much more expensive than comparable cities in the state.

Any suggestions on other directions we might go? Or, are there alternative methodolgies for accomplishing a greater cost capture? What are your cities doing?