Historically, Khorne has been the most influential and powerful god of Chaos due to the constant state of warfare the galaxy finds itself in. However, that position is not as total as one would think. Nurgle is by far the most variable of the gods and his strength waxes and wanes as his plagues spread and are cured. At his height, he can easily challenge and defeat Khorne, though at his weakest even Slaanesh bests him.

Going farther back, the truth is that Tzeentch, the Changer of Ways is the most powerful. Using his Crystal Staff, he possessed power unmatched by the other gods. This was a problem for him because it gave the other gods an enemy to ally against. Tzeentch sought to prevent this attack, so he broke his staff and weakened himself voluntarily. Without a much more powerful enemy, the alliance between the other gods collapsed.

Overall though, Slaanesh is by far the weakest of the Big 4 and Malice/Malal is the strongest secondary god and also the only one who can enter the Material Realm.

Sources: The Liber Chaotica (specifically the tomes of Blood, Fate, and Pestilence) the Labyrinth, the Codex of Chaos

Let's take an in-depth look at this shall we?

There are the five main chaos gods: Khorne, Nurgle, Tzeentch, Malice, and Slaanesh. Now I may be only a part time Librarian, but according to my studies I believe Tzeentch is by far the most influential.

Though Khorne's powers are definitely the most grand and terrifying on, say, a sub-sector scale, and Nurgle's are the most devastating in the long run Tzeentch really tops the cake.

Let's look at history and some of the largest chaos events known of and who was behind them (all while ignoring Malice because it basically just sits and seethes beyond the reaches of the Astronomican and Slaanesh because he just messes with the Eldar and looks at himself in the mirror all day). Now Khorne is incredibly violent, having covered worlds in a tide of daemons and blood that not even the Imperial Guard or Space Marines can stop, but that's all he does. Khorne is incredibly short-sighted in his plans, living only to add another couple million skulls to his throne and never planning ahead far enough to gain a legitimate foothold.

Nurgle however thinks a bit farther ahead. He merely lets his diseases run amok on worlds as he watches and gloats from his accursed bloat-throne. As his champions spew forth from pools of bile all over a planet he just creates more disease and watches the havok. Then again, not very far-looking, but still effective.

The perfect example of Khorne and Nurgle and their flaws is the Gheistos Cataclysm. For those of you who don't know, Gheistos was an agri-world which was taken by chaos early in M41. It all started with Nurgle infecting a poor agri-worker. This worker was corrupted by chaos and used an ancient spell in a fit of anger to summon thousands upon thousands of flies. These flies were Nurgle's playthings, each infected with the Black Pox. The shiftmaster near the boy was infected and ran away while the boy turned into a portal into Nurgle's realms, where his army was awaiting the call to action. With the Black Pox spreading every person in the Agri-Complex was soon infected with the black pox, and many turned into plague-soldiers of Nurgle. We know what happens now, planetary garrison alerted, Adeptus Sororitas arrives, etc.

Soon Nurgle convinced Khorne to join in on the blood shed, and so they forced the rift wider, and dozens of daemons started pouring into the agri-complex. Soon the daemons were pushing up into the Planetary Governor's airtight fortress, so he called for help. Soon the Vorpal Swords answered the call, striking the daemons where they were weakest. Khorne got annoyed and so opened up the skies with his sword, releasing a flood of blood which swept away all but the daemons and the Adeptus Astartes. Within three weeks the Grey Knights arrived, and pushed back the flood of daemons; Khorne and Nurgle were most displeased when Exterminatus was declared on the planet. Nurgle lost his newest plague, and Khorne (nor Slaanesh) had gained a victory.

Notice who wasn't present? Tzeentch. He was just sitting in his own palace watching his places go together. Tzeentch doesn't normally reveal himself because, unlike the other fickle gods, his plans stretch untold millennia, and he will win. If Tzeentch forces are present you know that he will win the battle because he already won a thousand years ago with planning. He's not the kind of god who kills for the sake of violence, because he kills for victory in the long run. Eventually Tzeentch will drown the galaxy in a tide of horrors, consuming it until every world is a warp-ridden waste and he has subdued every other race in the galaxy.

But personally I like the Tyranids more.