Tom's Doctor having the longest run seemed to face most of monsters, but was there some creature or foe that Tom didn't face that you wished he had?
My list:
Ice Warriors ( maybe during a return trip to Peladon?)
The Celestial Toymaker
Yeti
honorable mention: not a monster, but it's a shame they stopped doing straight historical stories. Would have been fun to see Tom's Doctor crossing paths with historical figures.