Paulie's shoes, Junior's schemes, after the jump ...
This is how "Sopranos" makes us laugh: Paulie getting out his shoes, one white pair after another; Junior and other nursing-home residents singing "Take Me Home, Country Roads."
This is how it makes us ache: Tony actually considering whether he should kill Paulie, and it's not even because Paulie might betray him; it's that Paulie annoys him. Junior, once the big man, taken down by a crazy kid emulating Junior's own craziness. And when we see that Paulie and Junior are alone and for the most part unloved, we see that's probably what awaits Tony.
Paulie may think of the killing of Big Pussy when he gets on the boat with Tony, but we should also think of "The Godfather, Part II" and the killing of Fredo. It's also on the water, it also involves a character who is both a liability and a loved one, and it's a killing that removes one more connection of another character to humanity.
When Michael in "G II" has his brother killed, he has shown once and for all that he will do anything to protect his power and standing; it's the moment that makes "Godfather III" superfluous, because Michael has lost his soul there.
When Tony ponders killing Paulie, he knows on some level that it could destroy his soul -- and Tony, whatever me may think of him, still believes that he has a soul. He keeps pressing Paulie on the Johnny Sack situation because Paulie's confession could be considered betrayal, and therefore a rationale for death. (Fredo, remember, had sealed his fate by disloyalty to Michael.) But Paulie knows that you never admit to anything, and Tony can't quite bring himself to kill Paulie just for being a pain in the neck. And then, of course, regrets it because Paulie is still a pain.
And then there's Junior, showing us what faces Tony down the road if he lives long enough, especially if he outlives his enemies or is no longer a threat to them. No family, no love, no escape, just sadness, small schemes and a daily dose of meds. He can still win admirers -- but they're all crazy. Sane people will just drain him. (And, in Tony's getting a "bridge loan," there's the suggestion that Tony is already feeling drained.)
Making this all even sadder is that Tony's decision not to kill Paulie also suggests, not for the first time in the show's history, that he doesn't have the stuff to run the mob. He's not quite ruthlessness enough. His violence can be capricious -- witness the fight with Bobby earlier this season -- instead of calculating. Michael Corleone would never make such a mistake.