For those (like me) who can't remember what Stardate something occurred on, a rough index by entry follows for those looking for a particular story arc.
Alexander (Platonian) - Log entries 83-86, 89-90, 92, 146, 165, 170-173, 201
Assassination attempt on Scotty - Log entries 72-78
Birth of Leonard James Akaar - Log entry 65
City on the Edge of Forever - Log entries 123-145
The Conscience of the King - Log entries 310-335
Death of Akaar - Log entry 63
Death of Crater's Creature - Log entry 29
Death of Eleen - Log entry 67
Death of Ensign Garrovick and dikironium creature - Log entry 209
Deaths of Ensign Mitchell and Lieutenant Franks - Log entry 9
Death of Harry Mudd - Log entry 255
Death of Kodos/Anton Karidin - Log entry 331
Death of Kras - Log entry 67
Death of Lenore Karidian - Log entry 332
Death of Lieutenant Krueger - Log entry 144-145
Death of Lieutenants Kemp and Latimer - Log entry 362
Death of Parmen - Log entry 88
Death of Vians - Log entry 12
Deep space stations surveys - Log entries 162-164, 166-169
Destruction of Yonada - Log entry 159
The Devil in the Dark - Log entries 175-194
Disgruntled/traitorous/not terribly bright crew problems - Log entries 14-15, 47, 276-279
Elasian tears (based on Elaan of Troyius) - Log entries 280-295
The Empath - Log entries 4-17
The Enemy Within - Log entries 94-104
For the World is Hollow and I Have Touched the Sky - Log entries 147-160
Formation of Amanda Station - Log entries 190-195
Friday's Child - Log entries 58-69
Fun with Androids - Log entries 256, 260-266, 274-276
Gamesters of Triskelion - Log entries 343-350
Gem - Log entries 8, 10-13, 15, 18-22, 45. 79, 92, 122, 156-157, 170, 172-173, 266, 278, 339
I, Mudd - Log entries 241-255
Interrogation/Death of Lieutenant Lagen - Log entries 74-77
Joanna McCoy - Log entries 38, 45-46, 48-49
Klingons - Log entries 52-54, 58, 60, 62, 64, 66-71, 106-108, 118-120
The Man Trap - Log entries 23-32
Mirror, Mirror - Log entries 49-56, 296
Pike - Log entries 34-40, 42, 73-44, 273
Mudd's Women - Log entries 106-121
New Years 2261 - Log entries 1-2
New Years 2262 - Log entry 365
Nova, Minarian - Log entry 17
Nova, Triskelion - Log entry 350
Obsession - Log entries 201-210
Plato's Stepchildren - Log entries 78-90
Professor Crater's Trial/Execution - Log entries 40-41
Raw material searches/acquisitions - Log entries 175-181, 200-202, 213
Shore Leave - Log entries 297-307
Squire of Gothos - Log entries 216-227
Starbase IDSS K-12 - Log entries 37-46
Starbase Trap - Log entries 265-273
Winterfest - Log entries 351-364
Winterfest preparations - Log entries 340-342
