I've been trying to think of every story in which Tom's famous jelly babies appear. I believe the stories where they make an appearance are: Robot, The Ark in Space (feature quite a lot), Revenge of the Cybermen (when Kellman empties the Doctor's pockets), The Face of Evil (with the famous "I'll kill him with this deadly jelly baby" line),The Robots of Death, Talons of Weng Chiang (the Doctor's seen eating them briefly),Image of the fendahl, The Sun Makers, The Invasion of Time (feature strongly in that), The Pirate Planet, Destiny of the Daleks, Nightmare of Eden and The Horns of Nimon. That's 13 appearances altogether. Strangely they never appeared in Tom's last season (JN-T's policy of eradicating the humour from the series probably).
Interstingly the jelly babies first appeared in The Three Doctors, offered by Patrick Troughton's Doctor.
Tom also occassionally favoured other sweets, such as Liquorice allsorts (The Pirate Planet), humbugs (The Sun Makers) and ball bearings (Androids of Tara).