In many cases, Star Wars actually beats Warhammer technology wise. Especially in space combat. Breaking it up into four categories for space, and four for ground, it doesn't look too favorable for the Imperium of Man.
Shields:
Star Wars ships rely on the ever-popular deflector shields. They simply absorb the impact and prevent the energy or damage from reaching the ship. Against the continuous bombardments that SW ships favor in space combat, this is efficient as it provides protection for as long as your generators can hold out, and will recharge whenever the bombardment stops.
40K, on the other hand, relies on Void Shields. These are hundreds of layers of weak shields that simply transport whatever hits them to the warp. Against the broadsides favored by 40K ships, this is quite effective. The layers of shields will allow them to remove most of the incoming fire from existance. However, the flaw with this method is that any large hit will collapse the layer. Useful in 40K, where most hits qualify as large, but not as much against SW's continuous volleys.
Victory here goes to Star Wars, as their shields would have time to restore between volleys, while 40K shields would crumble under the continuous assault and be overcome quickly.
Size/Armor:
Now, in size, the Warhammer universe wins easily. Star Destroyers are one of the largest Imperial ships, and they only are 1.6 Kilometers long. Warhammer ships tend to average at six, with the capitol ships (the same role the Star Destroyers play) averaging somewhere around ten. This means more gun batteries, and more armor to burn through to reach something valuable.
On the matter of armor, Warhammer wins again. IoM ships are built to withstand massive punishment while their shields are recovering, and their armor is often stronger than their shields. Star Wars ships tend to be doomed if their enemy is still alive after their shields drop, as their armor can be pierced by a single fighter firing blasters, not to mention ship to ship weapons.
Victory to Warhammer.
Maneuvering:
Star Wars has the Hyperdrive. This device allows a ship to accelerate to FTL speeds, during which they are safe from all harm barring miscalculation. They know, often to the hour, when they will arrive, and the only limiting factor is that they have to get out of the way of obstacles, which is a mundane part of a jump.
Warhammer ships, on the other hand, jump through the warp. Not only is your arrival time dictated by the whims of fate, but whether you arrive at all is a gamble. Ships can be lost in the warp very easily. Even those that aren't can arrive at their destination months or years out of place. Ships can even arrive before they leave, or spend a few months traveling only to find that it has been centuries on the outside.
For usefulness and efficiency, Star Wars wins.
Weapons:
Weaponry is a difficult case. Star Wars has an advantage due to the rules of canon, as what is shown in the movies takes presedence over everything else. And the movies don't bother to explain much of anything about how their technology works. Warhammer has the disadvantage that everything is equally canon for it, so the convenient RPGs like Rogue Trader explain quite a bit.
Warhammer weapon ranges are measured in thousands of kilometers, with the longer ranged weapons getting into tens and hundreds of thousands. As for Star Wars, we don't know. There's never really been a mention of getting out of range of turbolasers, so their ranges are hard to confirm outside of estimates that are quickly contradicted. The Space battles in Star Wars take place much closer together than in Warhammer, so it could be assumed that their ranges are shorter, or that the fleets were fighting closer so the audience could tell what's going on.
Firepower is another issue. The Effective Firepower of a turbolaser is never stated, and has been shown to fluxuate wildly depending on how much power is transfered to the battery. They also rarely explain how much of the power the batteries are using, so consistancy is impossible. I personally would assume that Turbolasers are on par with the Macrocannon, the primary Imperial ship-to-ship weapon, as they have been shown to vaporize asteroids. Imperial Lance batteries would be more powerful, as they are designed to burn holes through ships in one shot.
Possible victory to Warhammer, but can't actually say for sure due to vagueness of Star Wars' source material.
Space Summary:
Star Wars ships win in shields and maneuvering, and that's without mentioning that in sublight speeds, Star Wars ships tend to be more maneuverable. The advantage of shields could be negated by Warhammer ships having superior armor, which leaves it a toss up on which has better weaponry. Overall, Victory goes to Star Wars in Space.
Now for Land.
Weapons:
Star Wars is definitely at a disadvantage here. The primary weapon of warhammer, the lasgun, is compared in damage to a 50cal rifle, and goes for the realistic depiction of heat damage. Bolters, the other main weapon, fire 75cal explosive slugs that hit with the force of a small grenade. These two factors mean that any firefight on the ground will end poorly for the Star Wars fighters.
On the Star Wars side, the blasters are weak, inaccurate, and rather useless. Their only advantage is that they don't require reloading. The lightsaber, while effective, cannot deflect the weapons being used against it and the user would be at a disadvantage in a melee, as Imperial weapons are crafted of heat resistant Ceramite, which is designed to resist plasma weapons.
Victory to Warhammer.
Armor:
Guardsmen armor is designed to withstand the damage of a 50cal rifle, though doesn't offer any insulation from the impact. Space Marine armor is made of ceramite, and is described as being able to withstand tank shells. Their armor could also withstand a lightsaber, at least for a limited time.
Stormtrooper armor couldn't protect them from Ewoks.
Warhammer wins on armor.
Units:
Warhammer has diverse military units, both in infantry and vehicles. As an accurate list would take all day to compile and examine, I'm just gonna compare the ones that most effectively compare to the AT-AT, and the AT-ST. The God-machines of the Adeptus Mechanicus: The Titans. Oh, and the Sentinel.
Well, easy one out of the way first. The Sentinel is a fast moving, light-recon vehicle. The AT-ST is a slower heavy-recon and support vehicle. AT-STs are equipped with a rotary cannon for anti-infanty, a twin blaster cannon for heavier armor, and a grenade launcher for everything. The Sentinel, depending on varient, can be equipped with flamethrowers, heavy lascannons for anti-vehicles, or basically any heavy weapon in the Imperial Armory. As a result, they can be specialized to handle their role much more than the AT-ST, but are much less flexible in battle. In base comparion, AT-ST wins.
Now, onto Titans and AT-ATs. Both the Warlord titan and AT-AT stand at about 22 meters, so we'll compare them. In battle, they have the same role: cracking open the enemy line and breaking everything inside. For this purpose, an ATAT is equipped with two medium and two heavy cannons. At long ranges, it can utterly wreck a defensive position. However, it is not very maneuverable, and lacks any secondary firing angles, meaning it can't defend against being outflanked. Warlords are built in the shape of a person, somewhat, and are equipped with incredibly powerful ranged weapons, often Volcano Cannons and Mega-bolters. They also possess point defense autocannon and Lascannon turrets to protect from infantry. If outflanked, the top portion can swivel at the waist at a moment's notice, allowing it to respond easily.
On a more minor note, the Imperium favors letting numbers and powerful weapons carry the day, often drowning enemy armies in a sea of bodies and bullets. Star Wars tends to favor more minor battles, with even the clone army being few in number. Victory goes to Warhammer.
Powers:
And now we compare the special abilities wielded by each side. Warhammer has the Psykers with their warp powers, while Star Wars has the Force.
Psykers are capable of ravaging battlefields with their abilities, warping machines and slaughtering enemies with rather horrifying powers. The most common method is through bio-lightning, though more gruesome methods are common. the downside is that Psykers have a tenuous grip on reality, and every use of their powers risks something more powerful taking notice and snuffing them out. If they're lucky. The risk of a psyker exploding and summoning a daemon into his own lines is a very real one.
The Force, on the other hand, is less powerful overall, but has no real risks when used. While what can be done with it is incredibly variable, it is a safe power to use, and can much more effectively turn the tide of a battle.
Victory to Star Wars.
Ground Summary:
Warhammer wins due to sheer firepower and intelligent construction. When Jedi or Sith enter the fray, the tide can shift against them, but their overall quality should carry the day.
