I was recently at my local gaming store and, while playing a game of my own, watched a couple tables over as a player using the new Thousand Sons and Magnus handily defeat a pretty competitive Space Wolf player, who himself was running Wulfen and lots of vehicles (I had lost to that same Space Wolf player in past games myself). Ever since he was released, I have thought Magnus would be a very competitive LOW choice for any CSM players and, the more I look at him, the more I think he is very tough to deal with, even for very competitive tournament armies.
Looking at his basic stat line, he has the following:
WS7 BS7 S8 T7 W7 I7 A6 Ld 10 Sv4+/4++ (Flying Monstrous Creature) — Costs 130 MBs
*Special Rules — Adamantium Will, Deep Strike, Eternal Warrior, Fearless, Fleet, IWND, PML(5), VotLW, Daemon of Tzeentch (so re-roll saving throws of 1), Omniscient Eye (has LOS to all units on battlefield when using Psychic Powers), Unearthly Power (harnesses WCs on a 5+)
*Wargear — Blade of Magnus (S: User, AP2, Force, Soul Blaze, Transmogrify –> 6+ to Wound causes ID and models slain by this become Chaos Spawn) and Crown of the Crimson King (4++ save and ignore Perils of the Warp)
On top of all this, Magnus know all 7 Tzeentch powers, all 7 Change powers, and the unique Gaze of Magnus power (18″ S: D AP1 Beam power which requires harness 5 WCs successfully). As you can clearly see, Magnus is very durable (T7, W7, EW, re-roll saving throws of 1, can Swoop as a FMC, and 4++, which can boost to a 3++ whenever he has a Blessing cast on him), mobile (all the mobility benefits of being a FMC), strong in close combat (7 x S8 AP2 attacks on the charge, all at WS7 and I7 with the ability to make them ID via Force)), and, most importantly, able to put out ridiculous amounts of damage in the Psychic Phase (i.e. using up to 5 powers a turn, with everything from activating his Force Weapon to taking control of an enemy unit and shooting other enemy units with it to multiple Destroyer strength Witchfire abilities).
So, all of this begs the question, how can non-CSM players counter Magnus? Today I will look at this question from the perspective of a Space Marine player. Specifically, I think you have to break this question into two parts: (1) how to counter Magnus if you have first turn, before he go into Swooping Mode and cast a Blessing to up his Invul save to a 3++, and (2) how to counter Magnus the rest of the game, when he will almost always be Swooping and have a 3++ save due to casting blessings:
 Countering Magnus when you have 1st Turn — This is the significantly easier option of the two, since you don’t have to Snapshot at him (or use a Skyfire weapon) and since he only has his base Invul save. Solid options for Space Marines include the following:
a) 1st Company Task Force — Since Magnus is not a GMC, he does not have FNP and also is still vulnerable to Poison Weapons. Based on this, 2-3 squads of Sternguard in Drop Pods from a 1st Company Task Force can DS in turn 1, target Magnus with Preferred Enemy (thanks to the formation Special Rules), and then unload up to 20 Poison(2+) shots per squad on him while he is still in Glide mode. With even just one Sternguard squad like this, they average 20 shots, 15-16 hits, 15 wounds, and 6-7 unsaved wounds, which with some luck with bring down Magnus in a single volley.
b) Skyhammer Grav Devastators — Like above, if you bring in two squads of Grav Cannon Devastators turn 1, they have 40 shots, 26-27 hits, 19-20 wounds, and 8-9 unsaved wounds on average, which should statistically kill Magnus in Gliding mode before he can even get into the game.
c) Two Predator Annihilator Squadrons — With maxed out squadrons giving them Monster Hunter, two squadrons of 3 Predators each can put out 6 TLed Lascannon shots and 12 regular Lascannon shots. This averages out to 13-14 hits, 12-13 wounds, and 5-6 unsaved wounds after Invul saves on Magnus… not quite enough to kill him by themselves, but this still brings the LOW down to 1-2 wounds, which the rest of your army ought to be able to finish off with reasonable certainty.
d) 10 TH/SS Terminators and attached Inquisitor (with Rad Grenades and Relic that allows Hatred once a game) and Librarius Conclave (with Electrodisplacement) — Drop Pod in a unit right next to Magnus turn 1 (say a Tac Squad), then have the Librarius Conclave to use Electrodisplacement to “switch” themselves/Chaplain/Hammernators with the Drop Pod unit and subsequently charge Magnus that same turn. The Stormshields will help the unit absorb Magnus’ attacks and then, with 30 TH attacks they will average 22-23 hits (thanks to Hatred), 18-19 wounds (thanks to Rad Grenades bringing Magnus down to T6), and 7-8 Unsaved Wounds, which will kill him before can do any more damage to your army in later turns.
e) Shadowstrike Kill Team with two squads of 8 Vanguard Vets (all with PF/LC combo) — Since the Raven Guard Talon Strike force allows you to bring in Reserves starting turn 1, and the Shadowstrike Kill Team allows you to auto-pass Reserve rolls, you can Deep Strike and charge with the Vanguard Vets on turn 1 (with the Scouts able to prevent them from scattering, if properly positioned). Magnus will kill on average 4 Vanguard before they strike, meaning that the remaining 12 models get to hit back with 48 PF attacks, 24 hits, 16 wounds, and 6-7 unsaved wounds on Magnus when the dust settles (so he would either be dead on 1W at the end of the combat, which makes him easy to finish off next assault phase).
 Countering Magnus when he is Swooping and has a 3++ — This is the much harder path to travel, especially since it means you have to get a very high volume of powerful Skyfire shots to bring Magnus down:
a) 6 Grav Cannon/Missile Launcher Centurions with Land Raider Excelsior and Culexus Assassin support — The LR Excelsior can “cast” Skyfire on the Centurions and the Culexus, if moved within 12″ of Magnus, can “turn off” his Psychic abilities (including downgrading his 3++ back to a 4++, since the Blessing on him would be cancelled). Taken all together, the Centurions can then put out 30 Grav shots which average 20 hits, 15 wounds, and 6-7 unsaved wounds on Magnus. Throw in the additional 6 Krak Missiles with 4 hits, 2-3 wounds, and 1-2 unsaved wounds and you should be able to bring down a Swooping Magnus in one shooting phase, with average rolling.
b) 10 Sternguard with attached Librarian (with the Memento-Mortispex Relic) and Culexus Assassin support — If the Sternguard squad can get within 12″ of Magnus, the Librarian can give them Skyfire ( with the Memento-Mortispex Relic) and cast Prescience on them, in turn allowing them to unload on Magnus with 20 TLed Poison(2+) shots. On average, 20 shots like this yields 17-18 hits, and 14-15 wounds. Provided the Culexus is also within 12″ of Magnus to downgrade his Invul to a 4++, then the Sternguard would inflict about 6 unsaved wounds, leaving the Tzeentch LOW with 1W left, which the rest of your army ought to be able to bring down.
c) Two full batteries of Quad Mortars from the Red Hunters Chapter, a pair of Stormhawk Interceptor, and Culexus Assassin support — The Quad Mortars can use their Chapter Tactics on Turn 2 to both gain Skyfire, which allows them to put out 24 x S8 shots, resulting in about 16 hits, 10-11 wounds, and 4-5 unsaved wounds (if the Culexus Assassin is within range of Magnus). That leaves 2-3 wounds left, which the Stormhawk Interceptors ought to be able to finish off reliably between their 4 x Lascannon shots, 8 x Assault Cannon shots, and 4 x Krak Missiles (all firing at full BS on Magnus).
As you can see, taking on Magnus with Space Marines is quite difficult, especially if he is Swooping and has his Invul save bumped up by a Blessing, but these are some ways to try and deal with him early in the game, before he can do too much damage to your force. If you do succeed in killing him early, you should have a strong chance of defeating the rest of your opponent’s army, since Magnus is about a third of the total points in a 2000 point game.