Here's what I can think of (some already mentioned):
TARDIS MISSING
1. The Celestial Toymaker - Taken away by Toymaker
2. Space Pirates - Separated by explosion
4. Genesis of the Daleks - Time Lords separate Doctor from his TARDIS
4. Android Invasion - TARDIS continues to Earth
4. Robots of Death - Taken out of mining hopper by robots
5. Mawdryn Undread - TARDIS goes to 1977, Doctor traveling separately stays in 1983
5. Enlightenment - Eternals hide it in the Doctor's mind (!)
9. Father's Day - Police Box shell is empty
TARDIS BROKEN UP
2. The Mind Robber - Broken up in Fiction Universe
5. Frontios - Broken up by Tractators
TARDIS NONFUNCTIONAL
1. The Daleks - Fluid link burned out (this happens again later)
3. (Much of the Doctor's exile through Three Doctors, but with exceptions like Colony in Space and Time Monster)
6. Vengeance on Varos - Out of Zyton-7 (enough reserve power to get to Varos)
10. Rise of the Cybermen - Damaged
TARDIS PRESENT BUT INACCESSIBLE
(Many, but notably)
1. Marco Polo - The Doctor loses the TARDIS to the great Khan in a backgammon wager!
1. The Aztecs - locked in a tomb
1. Dalek Invasion of Earth - buried under rubble
4. Destiny of the Daleks - buried under rubble
4. Full Circle - TARDIS carried off by marshmen
5. Four to Doomsday - Tegan accidentally moves the TARDIS into space
5. Time-Flight - TARDIS stolen by the Master
I'm sure I'm missing some interesting ones. There are more occasions where the Doctor is separated from the TARDIS during the course of the story, but it's not really important (e.g., Deadly Assassin, while he's in the Matrix).
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