I used GCTool and Wii Scrubber to wipe all the garbage bytes out of my ISOs (as well as to get the banner files for each of my games in case I could somehow use them with XBMC). The only big problem I found is that on my Windows 7 laptop it would have a read error every once in a while and would proceed to have strange problems if I didn't close the window and reopen it. It only happened every 15 or so open/close statements and didn't cause any issues with any of my games so it wasn't a problem.
Desktop:
OS: Windows 7 64 bit
CPU: Intel Core i5 3570K @ 4.4 GHz
GPU: EVGA NVIDIA GeForce GTX 550 Ti (Factory OC'ed)
RAM: 16 GB @ 1600 MHz
Dolphin Revision:3.0, 3.0-784, 3.5, latest 3.5
OS: Windows 7 64 bit
CPU: Intel Core i5 3570K @ 4.4 GHz
GPU: EVGA NVIDIA GeForce GTX 550 Ti (Factory OC'ed)
RAM: 16 GB @ 1600 MHz
Dolphin Revision:3.0, 3.0-784, 3.5, latest 3.5