GPU Tracker is basicly a frontend for the console clients which makes it easier to configure.
The V7 client is Stanfords new version of their folding software and they have said it is the only one to be recieveing updates/support in the future.
V7 automticaly sets it's self up at the beginning to run CPU or GPU or CPU + GPU. So for people just getting strated it is a good piece of software to use.
Before using either though you should get yourself username and passkey from the stanford site if you havn't already.