There seem to be two distinct types of slacker movie.
First, the buddy-movie (low brow slacker film). Typically, this type of slacker movie involves the travails and adventures of two friends after a McGuffin of sorts. The McGuffin is usually something particularly frivolous, which makes the slackers efforts to acquire the McGuffin that much more entertaining since they exert no effort to pursue something else that is more meaningful or productive. The characters are the slackers, but the movie itself tends to be frenetic and plot-driven. Also, drug use is usually prevalent, to amplify the aura of "slackerness" of the characters. The Cheech and Chong movies, Bill & Ted, Harold & Kumar, etc... are examples of such. Essentially, these movies are send-ups of the "road-movie," which are of course variations on the Odyssey.
Second, there are the atmospheric slacker movie (the high brow slacker film). These movies are more social in emphasis and tend to be more episodic. There is an atmosphere of lassitude and indolence. The characters have no goal. Bande a parte is an example (even though the two male characters are striving to steal money from the girl's house, most of the movie involves desultory set pieces).
I would imagine the origins from the second come from post neo-realism. Movies such as La Dolce Vita, or L'avventura, or the Leopard, obstensibly are social critiques, namely criticizing the aimless existence of the Italian upper-class. These movies also begat the French New Wave (Bande a parte capturing a similar mood, though less class conscious). Yet, the atmosphere and mood these movies convey are also crucial elements in many modern slacker comedies. The aimlessness of the Linklater films or the Gen-X films like Reality Bites, are basically variations of post neo-realism. Garden State kind of goes full circle with the main protagonist a drug induced emotional catatonic.
As an aside, you have a commingling of both genres in the Kevin Smith movies, since you have the buddy element with Jay and Silent Bob, or the two clerks, there is a sense of aimlessness. Neither buddies have any particular goals, and that is the subject matter of the film. But, the many humor of the film originates in the discourse between the buddies rather than the situation of the characters.
So, here is my thesis in an embryonic state. Older slacker movies would help to either support or contradict my ideas as listed above.
(an aside: both genres tend to be episodic in nature actually)