Here's one that works (kinda) and verification on more that don't.
TLDR: handguns, stealth, assault, and engineering the top perk doesn't appear to do anything. Like the William_Christop25 mentioned, crafting does, mostly.
Doesn't: "The Good, the Bad, and the Ugly", handguns. "After a successful Crit Hit with a Pistol or Revolver, damage and Armor increase by 30% for 5 seconds. +1% per Perk level."
Baselined with no applicable perks, then 1 point, then 60. Used a low damage pistol (12-15) to avoid killing things so I could crit the same target many times to see if there was a discernable effect in-game. Checked the game's reported values (weapon info and character stats for changes to damage or armor value) after the first crit, and then many crits in. Once I was satisfied with the data for the group, swapped to a high damage pistol that capped crit rate to finish everyone off with a crit (in case the crit needed to be lethal to trigger). Didn't see any evidence that supported an effect for any number of points.
Doesn't: "Toxicology", stealth. "Increases the duration of Poison applied to enemies by 5 seconds. +0.2 seconds per Perk point."
Tested with poison grenades (uncommon and rare), Venomous Fangs perk (all knives apply Poison), and a shotgun with 16% Poison Chance. With no points in Toxicology, for enemies that survived a full poison application, there were 10 tics (infrequently I'd count just 9, but I suspect if I'd captured video and counted after the fact I'd find I was just missing a tic occasionally). The number of tics for survived applications stayed the same with 0, 1, and 40 points in Toxicology. I also equipped the metabolic editor (heals while poisoned) and the timer stayed the same (5 sec) regardless of the points in Toxicology (in fairness to the perk, I'm not an enemy so Toxicology probably shouldn't increase the duration, it was just easy to check). Other interesting observations: Grenades dealt approximately half the damage per application (or per tic) as the weapons. Honorable mention, the perk "Neurotoxin" works with all the application methods I tried in exactly the way described - I'm sure the damage of a poison application probably scales to level (50 in this character's case) but it still was quite effective at killing normal mobs with several tics remaining (generally in 4-6) even with just a single poke from the common 37 damage test knife.
Doesn't: "Punisher", assault. "After defeating an enemy with a Rifle or Submachine Gun, weapon sway is nullified and weapon spread does not increase for 10 seconds. +0.2 seconds per Perk level."
This isn't a hill I'd choose to die on because "nullifying weapon sway" or "weapon spread not increasing" could apply to some situation that isn't obvious to me, but it didn't do what I expected (or anything that I noticed for that matter). I crafted a several different rifles, observed firing after a kill (with the rifle) down sight as well as from the hip with 0 and 1 point (the effect doesn't change with more, supposedly just the duration). There isn't an identifiable buff applied, I expected "weapon sway" to relate to the extent that the crosshairs drift, but that didn't seem to change in a noticeable way (and "nullified" seems like it should be obviously gone). As far as weapon spread, the crosshairs from the hip definitely still expanded as I fired or moved. Although it's tough to eyeball the spread, with Sandevistan active I didn't see anything about the trajectories of the bullets that leads me to believe the crosshair expansion was an error.
Does, mostly: "Crazy Science", crafting. "Increases the sale price of crafted items by 10%. +1% per Perk level."
At least the bonus points in this actually work, mostly. Points past the first increase the sale price, by about 1% of a base value, and vendors indeed purchase them for that increased price. Also the 2nd point in the perk appears to make the sale price 2% higher than the sale price for a character who's never had the "Crazy Science" perk. Which is also to say, I have no idea what the first point does. Comparing one character with 1 point in Crazy Science and one character who'd never had any, both level 50, the character without the perk actually had higher sale prices (and the % difference wasn't consistent, for some items the character with the perk was 1% lower, in others 2%). So there's some definite squirreliness that goes on with it. Other examples: The boosted sale price did not go away when I respecced and stayed boosted until I'd exceeded the previous # of points invested (at which point it began increasing again). Also there's some downright wacky stuff going on between the sale price amongst different saves, even different characters, because at one point my non-crazy science character was showing the boosted prices from the character who I'd left with 10 points in just prior to loading the 2nd save. On a different occasion, when I loaded a save for the first character (2 points in Crazy Science at that point) the sale prices listed matched the base values (100%) from the 2nd character who I'd just swapped from. Adding a 3rd point to Crazy Science at that point did make the prices change to 103% the base price. Tbh, haven't totally figured out the interaction but my guess is there's some table / set of variables that doesn't update completely unless you restart the game.
Doesn't: "Revamp", engineering. "Increases damage from Tech weapons by 25%. Increases charge damage from all chargeable weapons and cyberware by 10%. +1% charge damage per Perk level."
This one doesn't appear to work (or at least not particularly well). I used a couple of crafted Nekomata's, one with a large base charge multiplier, the other with none listed. Both crit capped so each shot was a crit. No damage perks aside from Revamp, Superconductor, and Up to 11. Up to 11 since I'd read that the "Feedback Circuit" cyberware didn't function without it and didn't want that screwing something up. My thinking for superconductor was eliminating armor variance should keep the damage ranges a little more consistent. I didn't notice much difference before / after adding Superconductor but there wasn't much before testing and it could just be a small effect in this instance since the Nekomata has pretty high damage per shot. Did several laps with each around Westwind Apartments aiming center of mass with fully charged shots and noted the damage ranges at 0 points, 1 point, and 50 points in Revamp (so roughly 60 shots per setup, not quite 400 shots total). The damage ranges stayed largely consistent within a little less than +/-10% of the average for each rifle which makes sense because the min damage per shot for the rifle is about 82% of the max. The rifles themselves did have different ranges b/c of the differences in charge multiplier and crit damage. I did note a very occasional hit ~10% higher than the usual max with 1 point and 50 points in Revamp. I suspect it had to do with rushing a little more and hitting off target in a more vital area, because the overwhelming majority of hits remained in the same range. Because of the weirdness with "Crazy Science" I actually re-loaded the 50 point test and did another lap from a fresh start, but no change.
"Merciless" and "Dragon Strike" not working was already mentioned, and the bit I've tested seems to support that.
