#1 - 43 
and #44
The following is a list of the 43 titles which made up the original The Three Investigators series plus the unpublished 44th title.  Click on a title to view scans of each of the published covers and to read detailed collector information about that title.

1. The Secret of Terror Castle
2. The Mystery of the Stuttering Parrot
3. The Mystery of the Whispering Mummy
4. The Mystery of the Green Ghost
5. The Mystery of theVanishing Treasure
6. The Secret of Skeleton Island
7. The Mystery of the Fiery Eye
8. The Mystery of the Silver Spider
9. The Mystery of the Screaming Clock
10.  The Mystery of the Moaning Cave
11.  The Mystery of the Talking Skull
12.  The Mystery of the Laughing Shadow
13.  The Secret of the Crooked Cat
14.  The Mystery of the Coughing Dragon
15.  The Mystery of the Flaming Footprints
16.  The Mystery of the Nervous Lion
17.  The Mystery of the Singing Serpent
18.  The Mystery of the Shrinking House
19.  The Secret of Phantom Lake
20.  The Mystery of Monster Mountain
21.  The Secret of the Haunted Mirror
22.  The Mystery of the Dead Man's Riddle
23.  The Mystery of the Invisible Dog
24.  The Mystery of Death Trap Mine
25.  The Mystery of the Dancing Devil
26.  The Mystery of the Headless Horse
27.  The Mystery of the Magic Circle
28.  The Mystery of the Deadly Double
29.  The Mystery of the Sinister Scarecrow
30.  The Secret of Shark Reef
31.  The Mystery of the Scar-Faced Beggar
32.  The Mystery of the Blazing Cliffs
33.  The Mystery of the Purple Pirate
34.  The Mystery of the Wandering Cave Man
35.  The Mystery of the Kidnapped Whale
36.  The Mystery of the Missing Mermaid
37.  The Mystery of the Two-Toed Pigeon
38.  The Mystery of the Smashing Glass
39.  The Mystery of the Trail of Terror
40.  The Mystery of the Rogues' Reunion
41.  The Mystery of the Creep-Show Crooks
42.  The Mystery of Wreckers' Rock
43.  The Mystery of the Cranky Collector

The Three Investigators' Book of Mystery Puzzles
44.  The Mystery of the Ghost Train  - M.V. (Mary Virginia) Carey and editor Eugenia Fanelli were working on this particular story when the series was canceled in 1987.  It is not known with certainty whether or not a manuscript still exists.  Ms. Fanelli was interviewed in the 1990's and again in 2010.  Although this story existed in a complete narrative form, Ms. Fanelli described the manuscript as "unfinished" to both of the researchers who interviewed her because she felt that "it simply was not a good mystery".  She rejected the story for publication and was working with Ms. Carey to revise the manuscript into something that could potentially be published.  Ms. Fanelli and artist Robert Adragna both confirm that cover art for "Ghost Train" was never commissioned for this story by Random House.
*My thanks to Tom Calhoun, who interviewed Ms. Fanelli in the 1990's, and to a very dedicated private T3I researcher, who extensively interviewed Ms. Fanelli in 2010, for providing information on "Ghost Train".