As far as I can tell, the most important scene that was included in the TV version but left out of the DVD "extras" disc is one that follows Hagen's call to Bonasera after Sonny's assassination. In this deleted scene, Bonasera is getting dressed to meet the Don in his funeral parlor. He complains bitterly to his wife, thinking that the Corleones have killed someone so important that they need him, a registered undertaker, to bury the guy--and then the other families will come after him. "I curse the day that you and Commore [Godmother] Corleone became friends," he concludes. Very dramatic!
On the other hand, the DVD set includes a brief look at Kay, wearing a mantilla, lighting candles in church. Though I can't be sure, I don't believe that scene was included in the TV version. It's important because the novel notes that, following the Great Massacre of 1955, Kay took instruction in the Catholic Church so she could go with Mama Corleone every day and light candles for her her husband to save his soul.