Best one I've heard was from a co-worker who stated "you're an atheist? So what do you believe in - science?" (with a sarcastic overtone on the last word).
The rest of the conversation was based around the usual arguments that science keeps on changing it's position with me responding in the affirmative that with the presentation of new evidence science does indeed evaluate and, if required, change its position - unlike religion which will either ignore the evidence or attempt to change it to suit their beliefs.
This lead onto the classic statement that "you have to believe in something" and unfortunately no humour was seen in my flippant reply that I believe I'll have lunch now - but I did have lunch so at least my belief happened
A good reply to the "science is always changing" argument is one that Sam Harris brings up in "End of Faith"
With each passing year, do our religious beliefs conserve more and more of the data of human experience? If religion addresses a genuine sphere of understanding and human necessity, then it should be susceptible to progress; its doctrines should become more useful, rather than less. Progress in religion, as in other fields, would have to be a matter of present inquiry, not the mere reiteration of past doctrine.
Science changes and adapts because it aids in the progression of society. Society advances as science advances and science advances with the demands of society. Religion doesn't advance or contribute anything to society except outdated beliefs which has stunted societies growth.