Note: I made these names up myself, so apologies if they don't match up to the anime episodes or whatever you think they should be
called.
I put *'s around the cases I feel are the best.
Case 1: The Roller Coaster Murder / Shinichi's Transformation
Files 1-2 (1.1 - 1.2)
Part 1 | Part 2
Case 2: The Company President's Daughter
Files 3-5 (1.3 - 1.5)
Part 1 | Part 2 | Part 3
Case 3: The Two Idols
Files 6-9 (1.6 - 1.9)
Part 1 | Part 2 | Part 3 | Part 4
Case 4: A Bet and a Burning Festival Pyre
Files 10-12 (2.1 - 2.3)
Part 1 | Part 2 | Part 3
Case 5: Akemi and the Men in Black
Files 13-16 (2.4 - 2.7)
Part 1 | Part 2 | Part 3 | Part 4
Case 6: The Haunted Mansion
Files 17-19 (2.8 - 2.10)
Part 1 | Part 2 | Part 3
*Case 7: The Hatamoto Cruise Ship*
Files 20-25 (3.1 - 3.6)
Part 1 | Part 2 | Part 3 | Part 4
| Part 5 | Part 6
Case 8: Mysterious Presents
Files 26-29 (3.7 - 3.10)
Part 1 | Part 2 | Part 3 | Part 4
Case 9: The Armored Knight Meets the Corrupt Businessman
Files 30-32 (4.1 - 4.3)
Part 1 | Part 2 | Part 3
Case 10: The Men in Black on the Train
Files 33-35 (4.4 - 4.6)
Part 1 | Part 2 | Part 3
Case 11: Italians, Fish, and Masked Yaiba Action Figures
Files 36-39 (4.7 - 4.10)
Part 1 | Part 2 | Part 3 | Part 4
*Case 12: The Film Club at Sonoko's Country Villa*
Files 40-44 (5.1 - 5.5)
Part 1 | Part 2 | Part 3 | Part 4
| Part 5
Case 13: The Karaoke Murder
Files 45-48 (5.6 - 5.9)
Part 1 | Part 2 | Part 3 | Part 4
*Case 14: Shinichi's Mother?*
Files 49-51 (5.10 - 6.1)
Part 1 | Part 2 | Part 3
Case 15: The Sword and the Cabinet
Files 52-55 (6.2 - 6.5)
Part 1 | Part 2 | Part 3 | Part 4
Case 16: Detective Boys - Two Brothers
Files 56-58 (6.6 - 6.8)
Part 1 | Part 2 | Part 3
Case 17: The Festival Photos
Files 59-61 (6.9 - 7.1)
Part 1 | Part 2 | Part 3
*Case 18: Moonlight and Piano*
Files 62-67 (7.2 - 7.7)
Part 1 | Part 2 | Part 3 | Part 4
| Part 5 | Part 6
Case 19: Abduction of the Soccer Star's Brother
Files 68-71 (7.8 - 8.1)
Part 1 | Part 2 | Part 3 | Part 4
Case 20: The Night Baron at the Hotel
Files 72-77 (8.2 - 8.7)
Part 1 | Part 2 | Part 3 | Part 4
| Part 5 | Part 6
Case 21: The Bride's Lemon Tea
Files 78-80 (8.8 - 8.10)
Part 1 | Part 2 | Part 3
Case 22: Detective Boys - The Girl Kidnappers
Files 81-83 (9.1 - 9.3)
Part 1 | Part 2 | Part 3
Case 23: Kogorou's Judo Friends and Ping-Pong
Files 84-86 (9.4 - 9.6)
Part 1 | Part 2 | Part 3
*Case 24: The Yacht Club in the Mansion*
Files 87-91 (9.7 - 10.1)
Part 1 | Part 2 | Part 3 | Part 4
| Part 5
Case 25: Heiji and Shinichi
Files 92-95 (10.2 - 10.5)
Part 1 | Part 2 | Part 3 | Part 4
Case 26: Murder in the Library
Files 96-98 (10.6-10.8)
Part 1 | Part 2 | Part 3
Case 27: Dr. Ooyama
Files 99- (10.9-)
Part 1