I use a leaderless setup through HKN and I am able to cyclone/root up to three targets using my three boomkins. I have one button keyed to send "this is your focus target". Each time I push the button, a different druid gets the command (through the toggle function in HKN). Whomever is my master at the time highlights one enemy, I push the button. I then highlight a second enemy and push the button again. Repeat one more time and I now have each druid with a different focus target. Now whenever I hit my cyclone button, all druids know to cyclone their focus target.

Note that I am using assist for DPS and healing and don't every rely on the focus for anything other than CC. If you're using focus to follow or something else, then what I am doing will not work for you.

Originally I had this setup for arena. Ideally I'd be able to see all three targets and set the focus on two of them. Then I could DPS my main target, hit the cyclone button and hope they're withing LOS which would cause two to be cycloned and then go straight back to DPS. I may be abandoning that and only worrying about my master cycloning while the other two continue to DPS.