That's really hard to answer without tackling the classification question head on. Do you mean groups that "would have" been considered a domain if humans had been around at the time? Or groups that are in some sense different from other domains to the same degree those domains are from each other?
Whether we tag something as a domain also depends on its abundance and/or visibility. I bet if you take dug into microorganisms, you'd find tons that are as different from plants and animals as plants and animals are fun each other. But they all tend to get lumped in as "protists" or something because... we kinda don't care. I wouldn't be surprised if we somehow found out there were a lot of extinct critters in equivalent situations.
In my draft reply, I was going to add "is this even the right question", meaning "is the taxonomy more of a human construct than a natural one". It seems the answer is yes.
>Or groups that are in some sense different from other domains to the same degree those domains are from each other?
I'm not a biologist, and especially not a microbiologist, so you should take what I say with a decent chunk of salt. That said, microbes are so wildly diverse that that version of the question sounds a lot like "are there any big extinct clades of microbes", which, I don't know, microbes are pretty persistent. But probably.
As for macroscopic life, there are some Ediacaran critters like rangeomorphs and tribrachidium that (to my knowledge) are not conclusively associated with any existing domain. So who knows about those guys.
Whether we tag something as a domain also depends on its abundance and/or visibility. I bet if you take dug into microorganisms, you'd find tons that are as different from plants and animals as plants and animals are fun each other. But they all tend to get lumped in as "protists" or something because... we kinda don't care. I wouldn't be surprised if we somehow found out there were a lot of extinct critters in equivalent situations.