First one that comes to mind is Alec Baldwin (The Schweddy Balls episode).
Also, Kevin Spacey for the Star War auditions episode.
Maybe Steve Martin for the King Tut/Blues Brothers episode.
Definitely Christopher Walken in 2000 for the “More Cowbell” sketch (he won the 2001 American Comedy Award for it), and it would have been well deserved over Bruce Willis for Friends.
And, based on the love for Jimmy Fallon in the category, I suspect that several cast members that returned to host would have won, like Dana Carvey and Will Ferrell, especially since both of them received individual performance nominations as cast members when that category existed.
Note that, as I like to keep reminding people here, the “single performance” categories in the late 70s, which feel more like better categorization to me each year, included guest performers in sketch comedy shows, leading to wins for Jack Albertson and Cloris Leachman on Cher and Rita Moreno on The Muppet Show. SNL guest performers were eligible there, but never got nominated against the strong regulars of that time period.