City of Death! It is with Four and Romana II and is one of my absolute favorites. Douglas Adams shares a writing credit on it.

Also, The Mind Robber, because it is the good crack. It's rather strange, but really fun! And it has Two and Jamie and Zoe.

Other good ones are (in my opinion) are Tomb of the Cybermen (Two, Jamie, and Victoria), Castrovalva (Five, Tegan, Nyssa, and Adric), Terror of the Autons (Three, Jo and UNIT) and Survival (Seven and Ace) but there's actually tons of good ones out there. Those were just ones I remember watching early on and enjoying.