How can I list only sites that use a particular theme or plugin?

WP CLI is the easiest option here.

First, we want an array/list we can store the desired sites in:

results=()

Then, we get a list of all sites as a variable, and loop over them:

blogs=$(wp site list --fields="blog_id" --format="csv")
for entry in $blogs
do
    if [ "${entry}" == "blog_id" ]; then
        continue # skip the CSV header
    fi

Next, grab the sites active theme:

    theme=$(wp theme list --status=active --format=csv --fields="name" --url="${entry}" | sed -n 2p)

Here I’m using | sed -n 2p to get the second line of output in order to skip the CSV header.

Then, if the sites theme matches what we’re looking for, add it to a list:

    if $theme == 'mytheme';
    if [ "${theme}" == "mytheme" ]; then
        results+=($entry)
    fi

Then we close our loop

done

Turn our list into a comma separated string, and pass it to wp site list via --sites__in:

wp site list --site__in="${results[*]}"

We could also swap the retrieval of the theme and the check for a wp plugin is-active call if we wanted to filter by active plugin, e.g. wp plugin is-active hello

https://developer.wordpress.org/cli/commands/plugin/is-active/