Kakashi vs Yamato: Kakashi is frequently called the next in line for Hokage for a reason. He knows over 1000 jutsu, and when he does fight he seems to always have a new ability he uses, and not old one's. He is brilliant, and earned a MS. Yamato is a weaker version of the first, suffers from lower chakra like Kakashi, but also does not have a range of abilities per our knowledge outside of Wood. Sure he was born with a mastery of two/three elements, but his progress seems to be stalled at wood release abilities. They are both elite level ninja, but Kakashi was a prodigy before he got the MS. He has the edge at this point. Keep in mind Kakashi knows all of Yamato's abilities and Kakashi never uses the same exact jutsu out of Chidori, and knows thousands more.
Kakashi vs Kabuto: They were compared a LOT when the manga first came out, and for the first 150/200 chapters I would say. Remember, just because Naruto beat Kabuto means nothing, as Tsunade helped him. Kabuto was referenced to have the ability to beat multiple Anbu ninja at once. This only proves they are on or were on a simular page. Remember, this was before MS or Kakashi improving the Chidori. Kakashi got stronger and surpassed Kabuto at this point, but with Oro's DNA, Kabuto's unique Medical abilities (Which Kakashi really can't copy) and then Oro's quicker healing and Jutsu reach (As shown by Sasuke) Kabuto would win.
Kabuto vs Yamato: This would be interesting, although Kabuto gets the edge due to the logical train of thought, I want to say Yamato's reach of abilities may prove more impressive against Kabuto. Kakashi knows Yamato's abilities as they worked together, but the extent or application of ability is different from notes about other ninja from the bingo book. Kabuto will underestimate him. Wood mastery is very unique and has a large scape of uses as we have seen from the Team Seven Arc when Naruto turned four tails. The whole reach of the ability is yet to be shown to us or Kabuto. Even Oro's summon of the first showed anyone real wood-element abilities.
The last note I will give is Yamato would leave. He is analytical like Kakashi, and knows when he needs to pull out. Kakashi being stronger and knowing that he is hands down the strongest shinobi in the leaf outside of the Hokage and Naruto, would stay and give his life to stop Kabuto or hurt him. His life is frequently on the line and he is willing to give it if to hurt a strong opponent. Consider is stupid or gutsy, Kakashi is one of a different cut than Yamato, deeply because of upbringing/working on teams with children. Yamato would take the help of anyone who would give him the edge, or flee if it is the best option. I feel because of this and Kabuto being 'stronger' that he will not die. Captured? Maybe, die, odds are no.