What is your goal? There are obviously pros and cons of doing it either way. I say do BOTH.
General internet users hate creating a new login and they definitely hate being led down the process of signing up when all they wanted to do was comment on something or share it with Facebook.
Putting Facebook Connect button your homepage, if done tastefully and without creating more visual clutter, would increase sharing/tracking because it is a method that doesn't require much additional work for your users. It is familiar (unlike your site for most first time users, I'm assuming); it is something they are probably used before.
Putting Facebook Connect at the login or register point is also a good idea because it gives them another option that making a new account.
If you are looking for a good design pattern to follow, look at Goodreads.com.