Even if you find a method that’s 99% effective, which you won’t, you’re left with 70 million humans or more. 70 million commiserating, humping, breeding humans.
I disagree strongly with some of these, such as a geomagnetic reversal, which has happened hundreds of times in the past - yet never caused any mass extinctions (including of human ancestors, the last one occurring 780,000 years ago). So compasses might get messed up, but who needs a compass when we have GPS, which also tells you exactly where you are? The Sun might also produce another Carrington flare, but that won’t do much besides destroy most satellites and the electric grid (of course, millions would die as a result of the infrastructure damage, but many people would survive, people in areas without electric grids would never even notice anything aside from auroras). Also, as I said previously on gamma-ray bursts, they would only have a sterilizing effect on half of the Earth, with the other half being affected by the destruction of half of the ozone layer, which would recover in a decade or two; humans could still survive by avoiding all sun exposure and growing food in greenhouses (glass blocks UV, greenhouses would also help against the cool spell that would follow).
It’d probably most likely be something either triggered by humans or a result of war, but even most of those probably wouldn’t eliminate the human race. Unless for example, we made a bunch of factories to fill up the atmosphere with sulfur hexafluoride (assuming there is enough raw material) and trigger a Venus greenhouse effect, but not if we just went on our way until all fossil fuels are gone.
Another consequence of a nearby gamma-ray burst would be that the radiation would cause nitrogen-burning in the atmosphere, resulting in various nasty nitrogen oxides, some of which are opaque. If the burst is near the Equator, you could blot out the Sun over most of the planet, to give a long winter as follow-up to the initial flash-killing.
That’s why I mentioned the greenhouses as also being able to keep it warm. As for whether those nitrogen oxides (or other byproducts) would make the atmosphere itself toxic to breathe, it would depend on how much forms at low altitudes vs. higher up; many of the gamma rays would be absorbed before reaching the ground but enough would still get through to cause problems (although articles that I’ve seen focus mainly on the ozone depletion as the biggest killer).
"I ain’t finalizin’ and saying that they will, Baby John. I’m just sayin’ that they might." 
Just to be clear, are you allowing scenarios where all life is destroyed? Because if so, an impact large enough to disrupt the earth’s crust will kill every human, but the earth will continue to spin and the crust will quickly reform.
Originally I looking for a circumstance where animal life is destroyed to 100% totals – no humans, but perhaps still plant and/or bacterial “life” that would allow for the Earth to continue to evolve and spawn something anew in a few million years. Though I suppose if nothing else fits the bill, a cataclysmic event that leaves the Earth itself a lifeless rock will do. 
I guess you didn’t watch it all the way through to notice the… ahem, “improvised musical cue” in this video. 
The soundtrack of “The Great Gig in the Sky” was an inspired choice, especially timing the impact with the beginning of the woman’s singing. Perfect.
Oh, yeah. That video still gives me tingles.
theres a couple of ones here which haven’t been mentioned:
The anoxic event leading to lack of a breathable atmosphere would seem to do the trick.
“oceanic anoxic events may have been characterized by upwelling of water rich in highly toxic hydrogen sulfide gas, which was then released into the atmosphere. This phenomenon would likely have poisoned plants and animals and caused mass extinctions.”
Could wipe out all animal life but some plants and bacteria would survive.
A mechanism that would destroy at least all humans and probably most larger animals would involve a widespread mutation of one of our symbiotic bacteria such that it would start to produce prions. If the prions cause destruction of a vital organ, the result would be a progressive condition leading to death, like CJD (mad cow type spongiform encephalopathy). If the bacteria are not themselves directly harmful and the prion attack were subtle enough, the vector might very well not be discovered before the race was past the tipping point (like with CJD, where one just gets stupider until the breathing reflex is lost). And there is no known defense against prions, especially as the immune system is unable to even detect their presence.
We didn’t evolve from bacteria—rather, we seem to have evolved from Archaea, creatures that look just like bacteria, except they’re weirder. Archaea are known for their phyla of extremophiles—my candidates for the last lifeforms left alive in catastrophic environmental conditions that would wipe out all others (say a sulfuric anoxic event like the one mentioned above combined with catastrophically high temperatures). If Archaea evolved to intelligent mammals once, maybe they could again.
I don’t think a meteor that blocks out the sun for a decade would kill us. We know enough about growing crops with artificial light via that we could create small settlements that lived off of indoor grown crops until the sun came back strong enough to grow crops outdoors.
As far as a pathogen, there is genetic diversity in life that will prevent all of us from being susceptible. Even if every person on earth gets infected (unlikely) and even if it kills 99.9% of people, that still leaves 7 million people.
A giant meteor that turns the crust into lava would probably kill us (I don’t know of people could survive underground from something like that).
The planet getting sucked into a black hole, or knocked into the sun would kill us all too.
No, actually I specifically looked for that one, then linked to it. For exactly the reason you found. yourself. :p;)
Personally, I’d say we’re so pervasive and generally adaptable that the only non-planet-killing event that would get us all would be something that was targeted at us, specifically and continuously. So either Skynet or aliens, basically.
“This week is not the time to be making long term plans. Be wary of change and large, fast-approaching strangers”
An atmospheric transformation like Earth’s changeover to an oxygen atmosphere. Some organism evolves that pumps out something that renders the atmosphere unbreathable. Chlorine gas is one possibility I’ve heard; some mutant algae starts producing chlorine along with oxygen.
And of course, there’s always the Voluntary Human Extinction Movement, an environmental movement that encourages people to abstain from reproduction in order to bring about the gradual voluntary extinction of mankind.
The group states that a gradual decrease in human population would prevent a significant amount of man-made human suffering.
chuckles wryly At the rate I seem to be going, I might join the Voluntary Human Extinction Movement involuntarily. In any event, it’s an interesting read.