During the last session of my barely-begun WFRP3 game, we continued the Eye for an Eye adventure. Fairly early on, one of the characters climbed to the roof and said he was going to look down the chimney. I jokingly told him I was going to give him the Blinded condition due to the smoke in his eyes.

This raised the question: is it "kosher" for me, as GM, to give out Condition cards just whenever it might seem appropriate, or are they only intended to be applied when specific rules or actions invoke them?

If the situation warrants it you may hand out the condition. There are some mechanical cases that will specifically create a condition effect. But there's no rule that prevents you from handing out a condition based on the happenings in your story. That's pretty much what being the GM is about.

In this situation you could hand out the blind condition until he can remove the burning tearing smoke from his eyes. Naturally it'll probably go away after a several rounds once he's out of the smoke. If he could splash water in his face it could go away quicker. Just use your judgment and if it makes for an interesting situation go with it.