Okay, this is the sort of debate that me (WH40k) and my friends (SC) have debated on for quite a while now. Here's the facts that I've laid out for the Starcraft factions and their respective counterparts:

Terrans: Simply just Space Marines without the genetic enhancements, powerr armour, or common sense in general. If they went head to head, Space Marines would win. 100% As for everything else... Ghosts. Their nukes would do an adequate amount of damage, but as long as the Imperial Navy has a little something called "Exterminatus*", Terrans stand no chance against Warhammer in any way possible. In fact, I think they suck so much that I'm confident that even the Guardsman's flashlight can kill them.

Protoss: The Eldar would just camp these guys to no tomorrow. Just by facing the Farseer in combat, most of their Templars would be eradicated. The Dark Templars would probably be annihilated by the Ranger squads. As if that wasn't bad enough, Protoss probably won't be able to fight back against the Wraithlords, Falcons, and Fire Prisms that the Eldar would be pouring into the battle. The Warp Spiders are a bane against any infantry unit, and possess deadly grenades which would probably take out most Protoss vehicles in one shot. And the Archons? They would probably fight well, but since the Eldar are experienced with knocking out shields, they stand no chance.

Zerg: Tyranids would eat them for breakfast. Zerg might have numbers and broods, and Kerrigan as well, but compared to the Tyranids, they're small fry. Zerg can only convert Terrans into walking bombs. Tyranids take every bit of DNA they find and adapt it to their hive, whether it be poison resistance, chitinous armor plates, or organic acid cannons. Not to mention that the Tyranids also have organic hive ships about the size of most battlecruisers and they can spit acid, too. And they have creatures as big as an Imperator Titan**. According to Warhammer lore, almost every single world that the Tyranids came into contact with was utterly obliterated if there was not an EXTREMELY strong Imperial presence there to combat them.

-C0m1

*Exterminatus, in all terms saying, means exterminate. The Imperial Navy launches missiles from orbit that literally turns the planet into a barren rock, destroying every bit of organic life and utterly destroying the air.

**And Imperator Titan's height is somewhat akin to the Empire State Building. That's pretty darn big. Now just imagine if the Empire State had legs and gigantic cannons.