The first use of that effect that I know were Emmanuel Carrier's short "Temps mort" installations in Lyon in 1995. Here's a potato version:
I guess Michel Gondry saw those too, because later that year he does «Temthe video for Like a Rolling Stone, in which he adds morphing between the different still images :
He uses it again in 1997 for a (rather silly) Smirnoff ad, with a bullet stopped in mid-air:
Principal photography on the Matrix started in 1998; once it came out in spring 1999 everyone and their mother did rip-off and parodies.
The connection between that film and MBM I'm most curious about is the fact that Dangers said he was supposed to do the whole soundtrack...
My favorite use of that Temps mort / bullet time method remains Chris Cunningham's advert for Orange, in which he uses long exposures to fantastic effect :