Jim kept the dead man's identity a secret because the dead man was Huck's father.  Jim was afraid that Huck would leave him if he found out that his father was dead.  Huck was only running away to escape his father and Jim didn't want to be alone.
It creates a sense of futility in the entire adventure that Jim Huck and Tom have went on.  It also helps to explain why Tom didn't feel bad about helping Jim escape despite the fact that he doesn't believe that slaves are free people. It creates a sense of irony that the entire story was about helping Jim escape a fate that he had already escaped.  Last but not least it created moral ambiguity about Miss Watson.  Early in you could think of her as a mean person, but suddenly you realize that she wasn't a bad person and that she had the capacity to be kind to slaves.
Twain creates pathos by startling the reader into thinking that Jim is going to be killed.  When the townspeople bring back Tom, you are relieved that he is safe, but the feeling doesn't last long because Jim is following Tom and he is bound in chains.  They talk about hanging Jim, but thankfully they are afraid of the repercussions.
Huck comes to the startling revelation that Jim although being a black man, he is actually is a white man on the inside.
During these chapters 
Although Jim had recently regained his life and his freedom from slavery, and Huck had regained his friend, Tom was the most happy.  Although Tom gained the least from the excursion as well as managed to get a bullet through his leg he is joyous.  It is also ironic that he was happy that he got shot.  Although most people would be upset and frustrated if they got shot Tom is delighted that he has a battle wound to show off to everyone.  Tom isn't even worried about the fact that he might get an infection or get sick; he is just happy that he had a g
When Tom returns to the story, the story becomes more silly and light hearted.  When reunited with Tom, Huck suddenly reverts back to his younger self and returns to the hijinx that they used to get into comes back.
Nat and Jim are both very superstitious people.  They had both served as slaves, but Jim wanted to be free enough to run away.  Another difference between the two of them is that Nat is more easily fooled by Tom and Huck than Jim does.  Jim at least questions Tom's mischiefs, but Nat is willing to blame all of the problems on witches and ghosts.
There is lots of evidence to support that freeing Jim is no more than a game to Tom.  The first piece of evidence is that Tom doesn't believe that freeing Jim is the right thing to do.  Tom still thinks of slaves as less than him and he isn't friends with Jim the way that Huck is.  Another piece of evidence that this is a game to Tom is the elaborate escape plan that Tom has made up.  Tom goes over the top and does things that aren't even remotely necessary to free Jim.  Finally Huck and Tom manage to free Jim from his shed, but then they lock him back inside the shed.  
The Duke and Dauphine are finally found out as frauds by the town.  They are run out of the town.  Although Huck has known that they weren't real royalty for