GW at one point put forth some weird system that basically says "what if some ship crash landed on some feral planet where [WHFB] exists, and tried to take over?" Essentially you could get Chaos Knights wielding storm-bolters vs. elves with powerswords and Brettonian peasants with lasguns. Of course, such "technology" came as high pts powerups and whatnots, but the concept was there and quite flawed.
However, there is one things which fantasy has going for it: model count
I don't mean that the 40K weapons and rules and models could not handle the large number of models in the fantasy army, but rather, the fantasy rules focus largely upon the elimination of LARGE numbers of models. Our spells can cause 3D6 wounds and whatnot, and make things generally quite nasty for 40K armies who are typically about 50-100 models, and have unit caps of 10.
Furthermore, if the Fantasy rules were used, 40K armies would actually be obliterated in combat. Sure, those Chosen Terminators with powerweapons could kill a good many models, but as they are not ranked up, they are skirmishers and to not get a rank bonus, nor do they carry banners, and their armor's protection is decreased according to the strength of the models hitting them.
On a rules front, bringing a 40K model to a fantasy field is just plain idiocy.
On a fluff scale, it is quite the opposite. A .75mm explosive-tipped bolter shell would easily walk through several ranks of armor-plated chaos knights. It is stated in the gaurd book that feral platemail is essentially the equivalent of Imperial Gaurd 'Carapace' armor. That's a 4+ in 40K world.
Arguments of this nature just irritate the hell out of me, because it stems from a basic immaturity of the players. It goes back to schoolyard bickering involving "my daddy is stronger than your daddy", to which I always replied "so- i'm going to beat you senseless before your daddy gets here".
If you want to see who the better player is, play a game of 40K, and then play a game of FB, using FB rules. I promise that the Fantasy player will prove proficient in 40K 75% of the time, whereas the 40K player will often find himself horribly outclassed on the fantasy field. Not making generalizations, this is just what I've noted from personal experience.