Star Wars TOR had a great CE, too bad the game was kinda crap. Darth Malgus Statue Hardback Jedi Master Journal Sound track Maps Authenticator thing Steelbook Treaty of Corusant all packed in an awesome looking box.
Otherwise, I think that the Borderlands 2 had a very nice CE, as well as Fallout 3.
A Jose Canseco bat? Tell me...you didn't pay money for this. http://tinyurl.com/45pdkzf http://oi48.tinypic.com/ip48x1.jpg http://oi40.tinypic.com/8x7i8o.jpg
I can't objectively say best, because I don't own many. I'll list my personal favorite:
Dark Souls - it came in a nice tin box, had an art book, a digital download soundtrack, and obviously the game itself. Best part? It was only 60$ at launch. I got the collector's edition for the PS3 and X360 that night and it was worth it. The game itself is amazing, but you would have to have been a fool to buy the regular edition considering it was the same price.
Your name is sung and tattooed now on my heart - here I will carry you forever CarryTori Amos