A word with a checkered past
The word spook has traditionally been used as a sort of generic word for creepy creatures that wander about in the darkness—ghosts, bogeymen, ghouls, imps, and that sort of thing. Experts in the field of word origins compare the Norwegian word spjok (ghost—Danish: spøgelse, and in Swedish: spöke) and spiganis (Will-o'-the-wisp or corpse candle).
It is thought that there is a connection between the idea of 'to jest' or 'to scare' and this word. The Danish word spøg can mean 'to frighten someone as a prank.' There may also be a connection between this word and the English word spark.
Somewhere in the early 20th century, Caucasian racists decided to co-opt this term as a slur against blacks. The concept that black people were hard to see at night, thus linking them with evil night-stalking monsters, goes back into the misty past of race relations. The term is well-documented to have been in use since the early 1940s, but I have an earlier attribution for this slur.
In one of the Little Rascals shorts (Spooky Hooky, from 1936), the juvenile protagonists have to go into school after hours to deliver a bogus doctor's note to the teacher's desk so that they can sneak off to the circus the next day. The school proves a scary place after hours, and at one point, Buckwheat (the black child) tells his companions "They's spooks out there!" Causing his friend Spanky to quip "Oh Buckwheat! The only spook out there is you." Ouch. (This episode has since been sanitized, and the offensive line removed, but it is still available if you know where to look.)
Because of the racist overtones, the word fell out of favour, and now is pretty much restricted to the cloak-and-dagger meanings. I have actually seen instances on etymology discussion boards where young people were unaware of the other meaning of the word altogether, which I think is kind of nice.
References:
Africa Update Archives: http://www.ccsu.edu/Afstudy/upd4-3.html
Snopes.com online "What is the Etymology of the term Spook?" http://msgboard.snopes.com/cgi-bin/ultimatebb.cgi?ubb=print_topic;f=95;t=000880
Online Etymology Dictionary: http://www.etymonline.com/index.php?l=s&p=36
Dimivew assisted with a bit of linguistic aid
TV.com...I love what you can find out on the web