This is not a great answer
This is a very general question, with a specific example given, and this answer addresses the example very specifically. I think there are lessons that can be drawn from this answer, and I think this answer is probably useful to the question-asker, but it may not be as helpful to others with the same question, which was part of the intent in asking the question. I hope to see other answers that address how to handle the more general problem of intra-party imbalance in ways that do not focus too heavily on the specific example. I may also attempt to write one myself.
For now, though, this answer sort of straddles the line between the two questions. I’m answering in a very 3.x-specific manner, but that is because I think there are some issues based on the system that are worthwhile to look at. Primarily, determining whether you truly are the odd-man out, and if so why (from a system perspective).
First, just to put it out there: This is just reality in 3.x
The game, particularly at higher levels, becomes rocket tag. The ninja master failed to land his rocket (unsurprising, as Death Attack usually has low DCs and he was targeting a good save for you), so your rocket took him out. In reality, looking at your numbers, they are actually low for that level – as you say, you specifically avoided optimizing him.
Addressing intra-party imbalance
This is the more serious potential problem, if it becomes more and more difficult for the DM to challenge all characters equally at the same time. If someone you cannot kill in one round is all-but-impossible to kill for the other players, then you have a problem.
But you do comment that “they could deal out a hellacious amount of damage in a round too.” So if you are worried, the first step is to try to look at what they are doing. Can they keep up? If not, why not?
I suspect that the key, within 3.x, comes from your condition on that statement: “in optimal conditions.”
Power in 3.x comes less from whether or not you can one-shot opponents at high level (most people can), it’s more a question of how easily you can take your shot. In your case, you need to apply Samurai Challenge, but you can do that at range. Do the other players have similar capabilities? Are they all melee? Are the spellcasters familiar with the concept of attempting to target vulnerabilities (weak saves, touch AC, etc.), or do they rely too heavily on one spell or one type of spell?
These are systemic issues with 3.x, Pathfinder included, but I think the answer is not that you do too much damage: if anything, it’s that you can do your full potential damage more easily than your allies.
Your potential damage doesn’t look like a problem
More likely, the issue is that you can reach your potential more easily/frequently than your allies can
Without seeing the full character sheets, I cannot really give specific tips on how to fall in line with them, but for your own analysis of the situation, I think you should look less at the actual damage numbers – you are, after all, a primary damage dealer – and more at how easily your allies can actually follow through on their potential damage or effects.
Random other thought: hold yourself back, in character
A lot of players like to play a high-power character that they specifically do not use to its full potential unless or until things become truly dire. Support casters are a favorite for this: by focusing largely on buffs, you can let your party shine. Keep a few magic bullets in reserve in case something just needs to stop now. That sort of thing.
You could apply a similar strategy with your character. Samurai are notably honorable: perhaps your character feels dishonored for shooting a fleeing foe, even a dishonorable one, and resolves to avoid using his bow in favor of the more honorable sword duels. Restricting yourself to melee will drastically reduce your flexibility and ability to reach your full damage potential. You can hang on to the bow, however, and pull it back out when things are really rough: then using that bow becomes far more interesting from a story perspective, because your character was driven to do something he had foresworn.
Quick Explanation of Chat
In the comments is a link to a chat @mxyzplk and I had about the characters in the campaign, based on the sheets he’s linked. Basically, my conclusion was that his character, as the only pure-damage-dealer, deals an appropriately-larger amount of damage, and is not really mechanically overshadowing the other characters. Some player choices does lead to some characters not living up to the potentials of their mechanics, but it does seem that the group has concluded that mxyzplk’s one-shot kill is an expected outcome of the system and the fact that it was a glass cannon vs. glass cannon duel.
Some extraneous factors also appear to mitigate some of the larger issues with mxyzplk’s build. First, his sacrifice of Constitution in favor of Strength and Dexterity has not resulted in as large a loss of HP as it would otherwise entail, because he is allowed to reroll low HD rolls (and therefore has about a third more HP than he would otherwise, closer to the expected value of Con 14 than Con 10). Second, the campaign has tended to focus on a few, big enemies, rather than encounters consisting of enemy parties similar in size and level to his own. This has made the severe limitations on the Samurai Challenge much less than they would otherwise be.
So in conclusion, I maintain that in mxyzplk’s particular case described in the question, there isn’t really a problem at all.