These mass extinctions come typically every 20 - 100 million
years.
There are lots of different possible reasons why mass
extinctions could occur: climatological; geological
(plate tectonics could wipe out a bunch of habitats);
or even astronomical (next slide).
It has always been the case that the number of species
increases again after a mass extinction. One way to
think about this is that after many species die
out, there are many empty ecological niches into
which new families can adapt and succeed.
http://www.carleton.ca/~tpatters/teaching/intro/extinction/extinction1.html