The Gamecube saves are located in:
[Dolphin Path]\User\GC\
Wii Saves:
[Dolphin Path]\User\Wii
You could copy the files/folders over to the new one.
EDIT: Probably a better idea to copy the entire User folder over.
(http://forums.dolphin-emu.org/Thread-upgraded-to-dolphin-3-5-can-t-transfer-gc-mem-card-raw-files)
[Dolphin Path]\User\GC\
Wii Saves:
[Dolphin Path]\User\Wii
You could copy the files/folders over to the new one.
EDIT: Probably a better idea to copy the entire User folder over.
(http://forums.dolphin-emu.org/Thread-upgraded-to-dolphin-3-5-can-t-transfer-gc-mem-card-raw-files)
~ AwesomeMarioFan