Phil at Pyromaniacs writes about encountering his Evolution-Nazi professor during his college years. I can definitely relate to this one as well.
As he wrote, evidence can be very useful in these conversations, especially the omitted evidence or issues that get grazed over in order to support various pet theories. Some of my "presuppositional-only" friends scoff at the uses of evidential or classical apologetics. However, as a fairly new Christian who decided to go back to college to finish my bachelors and to get my masters degrees, I must say, I was very grateful to have the use of historical, evidential, and philosophical apologetics during most of my classes.
Yes, I was that annoying Christian who fearlessly asked questions not only for clarification, but also to expose falsehood and poor interpretations being taught. I know there were always other Christians in the class who were never going to speak up, or worse, perhaps having strongholds planted that needed to be exposed too. I like to think that the discussions were beneficial to all the hearers. (I do think I enjoyed the arguing/debating entirely too much :) )