I'd like to argue some of these because they are specific for certain champions. That doesn't make them amazing on everyone, but it doesn't mean they are worthless either.
Karthus, for example, loves Presence of Mind and Last Stand. Presence of Mind gives him 16-20 seconds off his ult on assist or takedown and it's off the base cooldown. So with his 200 second level 1 ult, if he gets a Penta, it's now 100 second cooldown. And unlike Ultimate Hunter that is multiplicative, this isn't. It's a flat 10% off your max CDR. So say Karthus somehow had 40% CDR at level 6. His 200 seconds is now 120. So getting that Penta now means his ult is on a 20 second cooldown. VS Ultimate hunter that would just make his ult be something like 102 seconds.
Additionally, Last Stand works in his passive state. So as he's dead, he can ult and now do 11% more damage to the entire enemy team regardless of what their health is. Should also work on other dead passives except Kog'maws since it's true damage. This is true of Kindred, Tryndamere, Kayle, and Taric's ults as well. This also works on champions like Teemo who might be dead and an enemy walks on their trap. Is it a must pick on everyone, no, but it has uses.
Biscuit Delivery isn't just free potions though. It's also permanent mana. If you're someone like Ryze or Anivia, or anyone that needs mana, these just add a little more. Even people like GP will take it so between the Biscuits, Klepto potions, and Mana flow band, they never run out of mana in lane before they get enough money for sheen.
Hextech Flashtraption was a thing on Zoe for a while. Because it's technically a summoner spell, so she could use it to have a ghost and damage from her W. Don't know if that's still a thing but I've seen it. Otherwise I agree, it's kinda interesting, but it's only really good on someone like Annie or Alistar. Someone who wants to flash in for a big play but can't because of it's long cooldown.
I do agree with some of the others though. Except for people doing a Tenacity troll build I don't ever see it. Plus we have so many knock ups in this game that Tenacity doesn't really do anything. I used to take Zombie ward on my supports for more wards essentially but it's not really worth it to spec into that tree for one rune. Never seen anyone use Unflinching. Might be good with Hexflash though. If there is a site that has the pick rates of runes it would be interesting to see which ones are ignored though.