First of all, excellent question!
I used to dismiss the potential for asteroid impact as a ridiculous Hollywood storyline. Then I took an astronomy course at the local community college and learned just how real a threat this poses. However, assuming there are no serious impacts in the near future, mankind will probably develop the technology to identify potentially dangerous objects and divert/destroy them before impact. So I doubt civilization will end this way.
No doubt there will be future disease pandemics, but mankind has repeatedly weathered these in the past and I see no reason why we wouldn't do so in the future. Same with earthquakes--I can't imagine a scenario where the number and severity of earthquakes would be enough to end life as we know it.
The black hole-particle accelerator idea is interesting but it reminds me of some of the similar predictions of potential doom when the first atomic bombs were being tested--probably more science fiction than science.
I'd say the single greatest threat is nuclear self-anhilation. Or possibly destruction or alteration of our environment at a rate faster than we can adapt to the changes.
Otherwise the Earth will continue being hospitable for life until it cools down sufficiently for its liquid outer core to solidify. Once that happens it will lose its magnetic field and eventually most of its atmosphere--ending up similar to Mars. But that still gives us billions of years to evolve physically and technologically--so who knows what might happen between now and then.