Been working through spreadsheet calculations for various jobs, finally decided to work on sam. (Note: Spreadsheets available here
Anyway, working through trying to find a 'best' option for sam is more complicated than for most since atmas and gear choices and buffs all interact. EG: A 4-hit can be made with VV atma if all you're getting is Haste, but fails once you start getting double Marches, in one particular setup. So general preconditions can have a notable impact on atma choice and gear setup.
That caveat out of the way, I'm mainly looking at seeing how much impact various atmas have in general to allow for more precise fine-tuning later on. I'm not going to do much gear tweaking, so actual 'best' results for a given atma can potentially be somewhat different that listed here.
Starting with Hagun for a baseline.
Preconditions: Haste only, no Marches or Samba. Hasso. Overwhelm always included. Berserk not used (in fact, just using /nin so as not to deal with subjob variances). Bison Steak. Lvl 97 target. 0.5 rounds average over-TP. Gear generally Unkai+2, and 5-hit to start with with gear used (+63 Store TP during melee, +16 Store TP during weaponskill).
No atma: 92.832
Demonic Lash: 100.999
Griffon's Claw: 103.130
Scorpion Queen: 94.993 (still 5-hit for Hagun)
Smiting Blow: 106.651
Stout Arm: 106.316
VV: 111.393 (still 5-hit for Hagun)
So Apoc looks strongest, followed by VV, followed by any of SA/SB/A&O/RR/Harvester. Keito with TP Bonus follows the same pattern since the higher TP per hit isn't quite enough to drop it to a 4-hit:
No atma: 104.593
(+10% WS Keito with no atma: 101.432)
Demonic Lash: 114.016
Griffon's Claw: 115.787
Scorpion Queen: 107.202 (still 5-hit)
Smiting Blow: 117.953
Stout Arm: 119.426
VV: 125.166 (still 5-hit)
And bumping up weapon delay again, using the Kikugosaku (480 delay, 5 str, 6 stp):
No atma: 102.514
Demonic Lash: 112.807
Griffon's Claw: 112.585
Scorpion Queen: 105.442 (still 5-hit)
Smiting Blow: 116.113
Stout Arm: 117.429
VV: 131.464 (4-hit)
Slightly weaker than the Keito except for using VV atma, where it's stronger.
Now for Keito with Store TP:
No atma: 97.888
Demonic Lash: 107.290
Griffon's Claw: 107.602
Scorpion Queen: 100.656 (still 5-hit)
Smiting Blow: 110.755
Stout Arm: 112.176
VV: 126.441 (4-hit)
In general weaker than the TP Bonus Keito, up until VV is added to reach a 4-hit, at which point it's on par with the TP Bonus Keito. Scorpion Queen isn't quite enough to do it on its own, as you'd need to add a lot of STP during weaponskill to maintain a 4-hit.
So overall it looks like Apoc and VV are the top 2 atma, though VV would lose a lot of its edge if not able to drop a hit (basically, falling back to about Harvester level).
Given Apoc and VV, what third atma works best with them? Using the TP Bonus Keito:
Demonic Lash: 173.434
Griffon's Claw: 180.710
Scorpion Queen: 165.617
Smiting Blow: 176.850
Stout Arm: 182.924
So top four contenders as the third would be Alpha & Omega, Stout Arm, Harvester and Griffon's Claw. Given how close they are I'd avoid A&O due to the -HP, so either of Stout Arm and Harvester would work. Smiting Blow loses out in this case because the weapon already gives +100 TP, so all over-TP is lost.
Trying again with the Kikugosaku (480 delay, 5 str, 6 stp):
~~ Interesting to note that while this was a slight bit weaker than the TP Bonus Keito with no atma or one atma, it's the stronger choice with two atma.
Demonic Lash: 179.748
Griffon's Claw: 182.942
Scorpion Queen: 171.965
Smiting Blow: 189.690
Stout Arm: 189.342
In this case A&O, Smiting Blow and Stout Arm are all neck-and-neck, and slightly ahead of Harvester. All atma choice are also generally better with this weapon than with the TP Bonus Keito.
Lacking Apoc, and thus starting with VV, what other two atma work best? Going to use the Kikugosaku again.
VV alone: 131.464
Demonic Lash: 142.517
Griffon's Claw: 145.723
Scorpion Queen: 134.468
Smiting Blow: 149.129
Stout Arm: 148.123
Here we see RR come back into play, nearly matching A&O. Without the triple attack of Apoc, damage becomes weighted slightly more towards melee (more rounds per weaponskill), which favors RR. Several atma end up coming very close as the second choice to go with VV. Aside from the slightly less safe A&O, RR, Smiting Blow, Stout Arm and Harvester are all fairly close. Given the probability of not being able to weaponskill ASAP when you have TP due to delays for !! procs, or trying to avoid ruby lights, RR gains a much stronger position.
So, combining VV with RR, the third atma choices:
Demonic Lash: 163.635
Griffon's Claw: 165.232
Scorpion Queen: 155.922
Smiting Blow: 168.639
Stout Arm: 169.264
A&O comes out the strongest of the remaining. If avoiding the -HP of that, Stout Arm, Harvester and Smiting Blow all come out pretty close a the third choice, though Smiting Blow starts to pull ahead the more you have to hold TP (up to a point). Griffon's Claw is slightly behind those.
Also: VV+SB+GC: 166.308
Slightly weaker than the others in this comparison, but I suspect it will pull further ahead once factoring in TP from regain in downtime plus Meditate and Sekkanoki.
In all these cases, Scorpion Queen comes out as a pretty weak option, however that's largely due to the gear setup where I already had enough Store TP that VV was pushing me to a 4-hit build. With more limited gear options (still starting at close to a 5-hit build using the Kikugosaku) Scorpion Queen becomes more valuable, and potentially outdamages Stout Arm/Smiting Blow/etc as third atma, and even comes fairly close to RR as choice for second atma.
Plaguebringer should end up being the same or slightly behind Scorpion Queen for all comparisons, assuming 'minor' DA is ~2%.
Don't feel like repeating all this for Fudo right now, so leaving it here. If someone else wants to take the spreadsheet and see what you can come up with, feel free. If you'd like a more narrow comparison based on certain types of gear sets, let me know.