We do similar to what dik suggests. Ours could be described:
1. Task takeoff -
Break down individual design tasks, meetings, travel, submittal reviews, etc. into small, manageable items and assign work hours to each item.
Calculate the personnel rates (those expected to do the work) times the hours and total the cost
Add direct expenses such as mileage, printing costs, etc.
Total the amount as the total design fee.
2. Percent of construction
This varies greatly from region to region and in different markets.
Basically there is a generally understood basic rate - such as 0.5% to 1.5% of the anticipated construction cost. In our area it seems to range between 0.5% to 0.75%.
3. By anticipated number of sheets
This takes some experience with your staff but you can slowly add records of how much time you spend on various sheets.
For structural you might keep records of how much time framing plans take, foundation plans, general note sheets, typical detail sheets, section sheets, etc.
For a project, estimate the number of each type of sheet you think will be provided and calculate the hours of each times the personnel rate.
You might even set up a range of values - so a foundation plan may take between X and Y hours depending on complexity.
Then when you estimate your hours you can assign a complexity factor to it to zero in on the best estimate for hours needed.
Once you have all three numbers above, your great, wonderful, imaginative, analytical engineering intuition kicks in and voila! You have your fee.