There've been a lot of characters featured in Star Trek across six TV shows and eleven (and counting) movies. Here's my list of the top fifty. If you think every series regular or all the most famous names you can think of will appear, you may be mistaken. To wit:
1. James T. Kirk (TOS, TAS, 8 movies)
Gene Roddenberry did not create Star Trek with Kirk in mind, but he's the captain who was featured in the version of the pilot that NBC liked, and the rest is history. Is there really any dispute that Star Trek would be nothing without Kirk?
2. Spock (TOS, TAS, TNG, 7 movies)
Kirk is the character who represents Star Trek, but the most famous character in franchise history is his Vulcan science officer, whose death helped make the movies popular and was essential to the 2009 reboot.
3. Jean-Luc Picard (TNG, 4 movies)
Only the complete opposite of Kirk could have led a new generation, and Picard introduced a new flavor to Star Trek, making Patrick Stewart an acting icon.
4. Q (TNG, DS9, VOY)
The unlikely breakout character from the first episode of The Next Generation was a trademark Star Trek omnipotent being whose use of sarcasm became legendary, helping him make appearances in the next two incarnations of the franchise.
5. Data (TNG, 4 movies)
Spock to Picard's Kirk, Data was the machine who wanted to be a man, and whose journey to realizing that goal proved a revelation in the Star Trek theme of exploring the human condition.
6. Worf (TNG, DS9, 4 movies)
The only Star Trek character to be a regular in two different series. Do I really need to say more?
7. Miles O'Brien (TNG, DS9)
Nearly as impressive is O'Brien graduating from recurring character to series regular.
8. Benjamin Sisko (DS9)
The grounding element of Deep Space Nine was its lead character, whose evolution matched the growing maturity of the series itself.
9. The Doctor (VOY)
One of the most fascinating personal journeys of discovery in franchise lore is the next step in concept originally represented by Data.
10. Charles "Trip" Tucker (ENT)
The most human character ever featured in Star Trek had his share of triumphs and tragedy.
11. Kira Nerys (DS9)
12. Kathryn Janeway (VOY, 1 movie)
13. Leonard "Bones" McCoy (TOS, TAS, TNG, 7 movies)
14. Odo (DS9)
15. B'Elanna Torres (VOY)
16. "Scotty" Montgomery Scott (TOS, TAS, TNG, 8 movies)
17. Khan Noonien Singh (TOS, 1 movie)
18. Seven of Nine (VOY)
19. Jonathan Archer (ENT)
20. Julian Bashir (DS9, TNG)
21. Lwaxana Troi (TNG, DS9)
22. William T. Riker (TNG, VOY, ENT, 4 movies)
23. Reginald Barclay (TNG, VOY, 1 movie)
24. Quark (DS9, TNG, VOY)
25. Dukat (DS9)
26. Deanna Troi (TNG, VOY, 4 movies)
27. Guinan (TNG, 2 movies)
28. Garak (DS9)
29. T'Pol (ENT)
30. Sarek (TOS, TAS, TNG, 3 movies)
31. Jadzia Dax (DS9)
32. David Marcus (2 movies)
33. Phlox (ENT)
34. Gowron (TNG, DS9)
35. Saavik (3 movies)
36. Nyota Uhura (TOS, 7 movies)
37. Wesley Crusher (TNG, 1 movie)
38. Malcolm Reed (ENT)
39. Borg Queen (1 movie, VOY)
40. Ro Laren (TNG)
41. Chang (1 movie)
42. Shran (ENT)
43. Geordi La Forge (TNG, VOY, 4 movies)
44. Tom Paris (VOY)
45. Christopher Pike (TOS, 1 movie)
46. Hikaru Sulu (TOS, TAS, VOY, 7 movies)
47. Jake Sisko (DS9)
48. Beverly Crusher (TNG, 4 movies)
49. Chakotay (VOY)
50. Kes (VOY)