When compared to SETI@home (not sure if that's a valid comparison, I apologize if it isn't) my GPU pulverizes my CPU in project-finishing (processing?) (see below for specs) while in F@H it's completely opposite; my CPU blasts my GPU out of the water. The TPF for my GPU would be multiple hours, whereas my CPU running only on two cores gets a TPF lower than ten minutes.
This is my setup/config at time of writing:
Folding at Home setup:
Two CPU cores working on project 8608, TPF 5 minutes 20 secs, ETA 7 hours 48 mins (at 12.30%)
Folding power Medium
SETI at Home setup:
Two CPU cores working on two tasks with names that are very long; my GPU "0.117 CPUs + 1 AMD/ATI GPU" also working on a very-long-name-project.
The differences between the GPU and CPU:
Elapsed time on CPU is ~25 minutes (they are within 5 seconds of each other), remaining estimate is 4 hours 35 minutes (they are within 30 seconds of each other). Progress complete (at time of writing) one at 6.8%, one at 6.7%.
GPU: Elapsed time is 18 minutes, remaining 20, at 50%.
On F@H the ETA for GPU would be close to 12 days.
I'm not sure if this is a problem or not.

Specs:
CPU: AMD FX-6300 Hexa core ~3.5GHz, not OC'd
GPU: Sapphire Radeon HD 6870 1GB OC'd to 1GHz core clock and 1.25GHz memory clock (OC'd same settings with F@H and SETI@Home)
RAM: 12GB G.Skill Ripjaws X Series, DDR3-1600, three sticks of 4GB.
F@H Version: 7.4.4/Latest at time of writing, 32-bit
SET@Home/BOINC Version: 7.6.6/Latest at time of writing, 64-bit
If anymore specs are needed, please let me know and I will be very happy to oblige.
If you need anymore spec details, let me know and I will be happy to provide.