my bread calculator
I know there are plenty of calculators and spreadsheets out there, but I wanted to share the one I use most often. You tell the basic parameters of your dough and it spits out the measurements: http://bit.ly/oyuT7Z 
My normal dough is lean with a yeasted preferment. I adjust the quantity if we have company and modify the hydration, flour types, and prefermented portion depending on what I ultimately want (pizza? rolls?), what I have in the pantry, and so forth. The spreadsheet tries to make this easy. You simply adjust the parameters at the top, and the spreadsheet spits out the recipe below for the preferment and final mix.
Right now the spreadsheet is defaulted to two 775 g loaves of Hamelman's rustic bread.
But let's say you want to make one 1000 g loaf with 5 percent whole wheat. Change the quantity to one loaf at 1000 g. Make sure the whole wheat flour percentage under "overall composition" reads 5%. How hydrated do you want the dough to be? Change that. What portion of flour do you want to be prefermented? Change that too. And so on.
You'll need to copy and save it as your own google spreadsheet to make changes. Just edit the colored cells, unless you want to really alter how things are calculated. Below I have some details on the measurement conventions I follow.
For you sourdough folks, although the lines say yeast the worksheet should work for you too: for the yeast percentage under preferment composition, simply enter your starter percentage.
I hope others find the spreadsheet useful. Please of course let me know if you have any suggestions, corrections, questions, etc.
Here are the conventions I follow. Bread flour is the base flour: that is, if you enter 0% for AP, RF, and WW, then the dough will be 100% BF. Bread flour is also the only flour in the preferment. I do not include yeast weight from the preferment in the overall yeast weight. The preferment baker's math uses the prefermented flour as the base weight. The final mix baker's math uses the final addition of flour as the base weight.
The fact that bread flour is the default preferment flour eliminates some degrees of freedom. You can't, for instance, have some prefermented dough (which necssarily includes BF), also enter 100% for AP flour, and end up with sensible output from the spreadsheet.