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This Top 46 was not edited by Chris Hanel, so it may not exude the subtlety and wit you're used to ;).
We weren't able to read all the entries (over 2000), so we chose the first 46 we liked. In future, we will close the Top 46 sooner, so we are able to read all the entries.
This list is not in any particular order.

1. Target practice for Darth Vader
   by Angel 17

2. The only useful application I've ever seen is the 501st...
   by doggans

3. The lone stormtrooper is easy prey. But when thousands are assembled, the sea of white armor acts as a defense mechanism, much like a zebra's stripes...
   by Peter Tutham

4. gettin chicks
   by ory

5. to hide Jango's hidden birth defect... the door marks on his head
   by darth_vaderess

6. Ever seen a stormtrooper naked?
   by ThePodSquad

7. Darth Vader can't choke the stupid one when he can't tell anyone apart. That's why he always chokes the officers.
   by JAR-JAR AND THE CLIFF

8. Tip the helmet upside down, fill it with water, and you got yourself a teapot.
   by Skaiwalkuh

9. Stormtrooper armor can be converted into a convenient, take-anywhere oven in just minutes, folks! And that's not all it can do!
   by Tycho Celchuuu

10. It's made to make the troopers confident enough to go into battle, and since none of them ever come back alive, no one's leaked the secret.
    by Max_Jaybo

11. Isn't it obvious? It's to make them a more presentable target! DUH!
    by Fwiffo

12. Ewok Trophies.
    by Fwiffo

13. Disguising yourself and your friends while you beat up a gaggle of Star Trek nerds.
    by tiene leche

14. Reflecting sunlight into opponent's eyes
    by rancor_fury

15. Mullet concealer.
    by Rin, Destroyer of Keyboards

16. It keeps them from splitting their heads on low doors.
    by Rin, Destroyer of Keyboards

17. According to Wizards of the Coast, it gives a damage reduction of 7 and an armor check penalty of -7.
    by Rin, Destroyer of Keyboards

18. Building thigh tone.
    by Keith

19. to hold the body together after it gets shot a couple hundred times (there is less of a mess that way)
    by Jaster

20. Ewok music instruments
    by fiskehandler

21. So troopers can lie to their wives. "No, baby, that wasn't me, I swear! It just looked like me."
    by Mab

22. TK-421: Wait ...this is armor ?!
    by BrenDarklighter

23. Isn't it obvious? Selling halloween costumes.
    by Munki

24. Japanese fashion shows
    by Rurouni Jedi

25. Cupholders on Star Destroyer bridges
    by Darth Cheered

26. Limiting the overall dexterity of their wearer.
    by Peregrin Toker

27. If you got beat by Ewoks, would you want your face seen?
    by Padawan Drew

28. Isn't it obvious? so the troops can die in some style.
    by HyperX

29. For those times when you just can't reach a bathroom
    by Jedi Master Joe

30. Ladies like a man in uniform...
    by Blah :)

31. Blaster Attraction
    by Jerad

32. To make sure the fridge and bath-tub don't get jealous
    by Nack the Weasel

33. Keeping drinks nice and cold in hot weather
    by Nack the Weasel

34. Hiding your wallet from those greedy jawas
    by Nack the Weasel

35. a surface on which to play tic-tac-toe while waiting for Lord Vader to finish choking the commanding general so we can get on with this stupid invasion already
    by NAHTMMM

36. To stand out in a forest so it will be easier to shoot you!
    by GTExcalibur

37. Recycling
    by Mungo

38. Low door protection.
    by khellhound

39. You can fry an egg on it once the Rebels are done shooting
    by Cardo

40. Making money on e-Bay
    by allthatsleft

41. When the Emperor wants to go bowling, round up ten stormtroopers and...well, you get the idea...
    by Captain EO

42. Vader can't see all the faces you're making at him.
    by ChrisZ

43. free lunchboxes for rancors
    by ISB Agent1

44. Um, sci-fi conventions. Yeah, it's probably useful for that.
    by Long-Gon Jinn

45. Not comfort, that's for sure.
    by Dracos

46. Container for McDonalds Big Breakfast.
    by Boba