Vengeance multiball: Hit the ship enough times and it'll open up. Hit it again to get a second ball. Hit ship again for multiball
Timing your shot for Warp 9.1 or 9.9 to coincide with any of the multiballs can pay off big with double scoring and big jackpots.
Klingon multiball: Complete green standups under side ramp to light locks. Lock ball in Enterprise of left saucer.
Modes can be completed during MB, so starting a mode before cashing MB is a solid strategy (esp. for Klingon, which covers all main shots)