Arnold Moss in TCOTK is a very underrated performance that gets overlooked a LOT - his 'reading' of Kodos' Final Orders is a wonder, and the interplay between him and Shatner is also very noteworthy. Then the genuine remorse he shows at the end when he realizes that he can no longer hide, and then the switch to horror as he realizes what Lenore has been doing is also pretty amazing.
But yes, between Windom and William Marshall as Daystrom, it is hard to pick which actor portrayed the particular brand of crazy needed for the show better:
Decker's horror at the mistake of sending his crew to the soon to be destroyed planet, and then grabbing the opportunity to commandeer the Enterprise and to get back at the planet killer is done so well - and its the little things: the Queeg-like juggling of the tapes; the disgust at having to order the Enterprise to veer off, after Spock pointing out he has to or be relieved; and the blank stare when talking to Kirk and Spock while awaiting his doom in the shuttle, and then waiting for the contact with the planet killer - girding himself, almost not being able to wait ANY longer for the release.
Then there is Marshall's Daystrom, a performance I just happened to see again YESTERDAY.. At first, Daystrom seems to be your basic nerd genius - a little awkward talking to real people, but also very proud and very, VERY protective of his invention. But when things start unraveling, he starts unraveling as well. almost like shedding layers of skin, revealing the madness within - which of course, happens to his computer as well!
One final thing - one has to be impressed with the work all through the series of Joe D'Agosta, who was Desilu's casting director at the time. Both on Trek, and on M:I, outside of the occasional Stanley Adams. he did a pretty amazing job casting both show's guest stars.