Keep the discussion going - what's the 40K version of the FTL?
Happy to oblige
The 40k universe is based on the existence of the Warp, a dimension which is parasitically (in a way) attached to ours. Within it dwell daemons, beings of the purest malevolence which exist only to devour and destroy the inhabitants of this universe. These parastical daemons have a great deal of power in our universe, but are limited by their ability to only break through into the flesh of a person "touched by the Warp"; basically, people who manifest psychic, telekinetic, or other powers and who are then noticed by the Warp creatures and corrupted.
The other way daemons can attack the humans and other races of our universe is when they enter the Warp to travel through space. This is different for each race in the 40k universe; humans break into and out of the Warp, and travel within it to cross the massive void between worlds. There is the element of travel inside it - as its been described in the few books to tackle space travel directly, the Warp is described as a maelstrom with currents and eddies - in my mind I imagine it looking something like the Badlands from Star Trek, only with a blue-purple colour palette.
Time is also not a definite factor within the Warp. Ships have entered for a three-week journey and come out two centuries later, or not at all, or indeed exactly when predicted. Navigation is carried out, for humans, by triangulation of the Astronomicons spread throughout the Imperium of Man (the majority of the Milky Way, although tenuously held at best). The Astronomicons are kept alight (they are described as powerful white lights cutting through the turbulence of the Warp) by the constant singing of psychic choirs. The psychically-attuned, mutant Navigators on each ship guides their ship by these lights and through the drifts and eddies of the Warp.
The human ships, while they are within the Warp, are the object of the intense need of daemons to inhabit hosts, making Warp travel exceedingly dangerous. The incursion of daemons onto ships is held back by the Geller fields (something which is never really explained - its just there), but other races do things different. Orks, for instance, when within the Warp just let the daemons come, and enjoy the bloody good scrap which ensues
The genius of this idea is that space travel, which is so utterly vital to maintaining an interstellar power, is also so incredibly dangerous and unpredicable. Warp storms have been known to cut off entire planets and sectors from communication and travel with the rest of the galaxy at random. The unpredictable nature of it makes for a wonderful setting in which to insert stories. The 40k universe will lack subtlety for seasoned sci-fi veterans, but the action contained within the best books rivals anything else I've read.