This isn't too structured in my mind, so it will come out rambling, but I wanted to express it anyway. Feedback would be awesome! (She said hopefully, even though feedback on Dreamwidth is rare indeed! But all the more welcome when it happens!)
Spoilers up through Rakuyo arc, and I'll edit the start of the post in case there are comments that go further. (I can't be spoiled, myself, since I've completed the manga.)
Among many other themes and repeating patterns, I feel like we have several interrelated ones to do with purity, impurity, and connecting/comparing yourself to others:
Let's start with Gintoki as a purifier, in spite of how often he is associated with impurities, in habits as well as in daily morals, neighbourhood, speech, and so on. (Of course this is mostly comical, but that doesn't make it non-relevant.) The Benizakura arc talks about swordsmiths purifying their souls as well as their swords, and Gintoki becomes Tetsuko's champion against Nizô who becomes less the wielder than the tool of the "impure" sword Benizakura. But it's Nizô and the sword's maker Tetsuya who are single-minded in their pursuit, "pure" in one sense of the word, while Gintoki explicitly celebrates the cares of ordinary life (telling Tetsuya, "You just didn't want to bother") and being his generally surface-dirty self in habits and speech as usual.
The Shinigami arc also speaks of purifying, but in terms of skilled executioners supposedly being able to purify the souls of those they're beheading, in a way that shows how Asaemon and her adoptive father viewed those condemned men as human beings, wishing for them to be purified of their souls at the point of death. Gintoki could have been one of those men, yet Yaemon Ikeda XIV helped him and other men he deemed innocent escape, which in the fullness of time obliges Gintoki to take up Asaemon's cause no matter how much she insists she shouldn't be saved. And I feel that it's strongly implied, again, that Gintoki also becomes a purifying force in the process.
As mentioned above, the consistent association with Gintoki and impurities seems to contrast with this. But so does Gintoki's repeated habit of equating himself with an opponent or someone he's trying to help in a seemingly negative way that manages to be a kind of reaching out. "We're both trash, you and I", "It takes a coward to face another coward", "A drunk is best dealt with by another drunk", and so on. He's in essence telling the other person, 'Look, you're just a shlub when all's said and down, and so am I. Maybe we can co-operate or maybe I have to fight you to stop you, but at the end of the day we're equals, I'm not any better than you. You're not alone.' In doing so he simultanously refuses to exalt the other when they behave inhumanely, yet also refuses to cut the other one off from a shared condition of sinfulness and, it's implied, connection to humanity at large. ("Humanity" in the wider sense that also includes Amanto, except for those Amanto who cut themselves off from humanity contemptuously.)
But how does that square with Shoyo's statement to Gintoki that "as a monster, you can't cut down a monster's sword", and to "be stronger than me, use the sword of a human"? There the similarity is no longer seen as a benefit, but a hindrance. Yet who can be more sinful than a monster?
Is this apparent discrepancy meant to point to a difference in philosophy between Shoyo and Gintoki, implying that Gintoki's stance is ultimately the better one?
Or is there no such discrepancy - because Gintoki's position on all those occasions is meant to affirm humanity in himself and the other person? A flawed, sinful humanity, true, but that just makes it more believable and hence more credible. While being a monster means you're set apart from other people, in fact you're not even seen as truly a person. (Or you don't see yourself as one.)
I don't have a clear conclusion, I very much invite comments!
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tonko for looking this over and correcting it! 
