Gamma Ray burst .... thought that exploding supernova or hypernova within 6000 light years could cause tons of radiation to hit the surface, probably wouldn't kill everyone, but, if it killed everybody on the surface, it might have enough impact to destroy civilization. Looks like happens only a couple times per billion years, so not very likely humanity will survive long enough to experience this.
Massive volcanism, poisoning the atmosphere, and bringing about a "volcanic winter" which would result in a very large scale extinction. Most likely humanity would survive this as well, at least for a while, but eventually, I'm thinking the species may succumb. Looks like these happen a few times per billion years, so in reality, humanity will probably not survive long enough to experience this.
Asteroid impact, most experts currently think that the impact at the Chicxulub crater was the root cause of the dinosaur extinction 70ish million years ago. Could pretty much have the same impact as Massive volcanism. Looks like events on this scale are rare, Only one known impact of this scale. Most likely hundreds of millions of years until something like this hits the earth again.
Global Temperature Change and Atmospheric Change
This may result in many deaths, but I don't think it will be "enough" to destroy humanity. We can adapt and while many may not survive, it would take a LOT of temperature change to result in human Extinction.
Global Virus
This will always be a problem, but it seems like there are always at least some people who don't get infected no matter what the virus is. This is a horrible problem, but not an extinction event for humanity.
Alien Attack
Not very likely. I'm sure there is other intelligent life out there, but the universe is HUGE. How would they detect life on our planet? How would they get to our planet? Then, how do they effectivly fight against the earth and keep all their ships supplied? I know there is a LOT to learn about physics, and there may be some sort of way in which we could build ships that travel greater than the speed of light, but, that doesn't mean that there's infinite fuel or infinite supplies, etc.
Nuclear War
Countries who have the nukes are generally trying to slowly disarm them. I think it's likely that they will be used again in the future, but, hopefully not in a large scale manner, where hundreds or thousands of warheads are used. If a full blown nuclear holocaust were to take place. I don't think the initial blasts of heat and pressure would end the species. I also think that the radiation/fallout wouldn't be enough to wipe us out either. However, The nuclear winter that could, in theory, result, would have pretty much the same devastating effects that volcanic winter would have. And that might wind up slowly wiping out humanity.
I think the most likely "end" of our species is continued evolution, where "people" in 1 million years do not look like "people" today, but are instead a different species. I think the odds of a "world ender" type of extinction event are low in any given year, and so, chances are we'll probably last for millions, or perhaps even tens or hundreds of millions more years until eventually something catastrophic happens.