The fee/donation at BTC Guild is per block. There is no difference in the way rewards are determined between BTC Guild and Deepbit, other than the fact that you pick your personal fee based on what additional features you want and what you feel its worth.
Deepbit taxes the block then feeds out the rewards
I sincerely want to thank you for all those chuckles. Also, I think I'm going to save this somewhere to prove to people how not knowing basic maths can cost you money...
Now, to prove to you (or at least someone who can actually do maths) that 3% off the total block reward is the same as taking 3% off each share (note that I chose fictional values to make it easy to follow):
Lets assume you were working on a block that took exactly 200 shares to solve. You contributed 100 of them.
On deepbit, you would get half of 48.5 BTC, which is 24.25 BTC ((48.5 BTC / 200 total shares) * 100 profit shares = 24.25 BTC).
On BTC Guild, if you donate 3%, 3 of those shares would be used for donation, the 97 others would be profit. Now, (50 BTC / 200 total shares) * 97 profit shares = 24.25 BTC...
Yeah, obviously deepbit pays more.