Because Lord Jim is told by Marlow, the tone of the entire novel pretty much depends on how he is feeling and thinking at any given moment.
Thinking is the key word here. Marlow has a tendency to ponder just about everything he sees, hears, and experiences. He is often puzzled by Jim, whose emotions and actions seem wildly unpredictable, so Marlow devotes a fair amount of energy just trying to figure out what in the world is going on in Jimmy's noggin. This makes for a thoughtful tone:
He was of the right sort; he was one of us. He talked soberly, with a sort of composed unreserve, and with a quiet bearing that might have been the outcome of manly self-control, of impudence, of callousness, of a colossal unconsciousness, of a gigantic deception. Who can tell? (7.1)
Jim is a constant source of fascination, amusement, and pain for Marlow, who can't seem to stop analyzing him. Marlow likes a mystery.
And like any solver of mysteries, Marlow asks Jim all kinds of questions. He wants answers and finds Jim's vagueness annoying, which causes an emotional flareup every now and then:
"Why don't you laugh?" he said. "A joke hatched in hell. Weak heart! [...] I wish sometimes mine had been."
This irritated me. "Do you?" I exclaimed with deep-rooted irony. "Yes! Can't you understand," he cried. "I don't know what more you could wish for," I said angrily. He gave me an utterly uncomprehending glance. (9.19-20)
The dude wants answers, and Jim is not cooperating. Nope, he's too busy pondering his own concerns, wondering what has happened to him and what will happen in the future.
Jim himself also reinforces the novel's thoughtful, probing tone, though he does so at a higher emotional pitch than Marlow. For all Jim's despairing outbursts, he spends as much time as Marlow trying to sort out what has and will happen.
We can't write off Marlow's interest in Jim's story as mere curiosity. Marlow seems to actually care for the young guy, and seems to miss Jim after his death. But is he mourning for Jim or is he grieving over the loss of something else?
Arguably Marlow misses the now-dead Jim, but he also seems to long for something Jim took from him – a sort of faith and hope in the sailor community. This sense of loss drove Brierly to suicide and Jim to despair, so it's no surprise that loss and longing make their way into the novel's overall tone.
We see this wistfulness most clearly through Stein, who relives his long gone glory days and mourns the loss of his dreams:
"And because you not always can keep your eyes shut there comes the real trouble – the heart pain – the world pain. I tell you, my friend, it is not good for you to find you cannot make your dream come true, for the reason that you not strong enough are, or not clever enough." (20.32)
Life at sea, while full of adventure, is a lonely pursuit. For these sailors, the reality never quite lives up to their expectation, and they're left to ponder their dreams in lonely old age.