Heyo,
I'd start with OSE and export the data compare it to GWT "Your Site on the Web" tab (specifically the Internal Links as well as the Links to your Site).
Then take a trip down to good old:
This is a great way to analyze Second Tier Links if the first site contains links with the secondary URL. Also consider analyze the anchor text with this process. Will probably take a bit of elbow grease, but this is a good start.
Good Luck and good on ya!
Shameless Plug: follow me @derZukunft on the Tweeter.
Cheers,
Brian
