I've always used a sticker (black dot-shaped) or a piece of post-it note. Post-it is really convenient but it's ugly. I still think the best solution would be

I've always used a sticker (black dot-shaped) or a piece of post-it note. Post-it is really convenient but it's ugly. I still think the best solution would be to have no builtin camera or microphone. Just have something like the iSight that you manually and thus willingly connect to your thunderbolt. Works with your external monitor as well and you can orient it the way you like. It would also have better overall image and sound quality (low light, more shallow depth of field, etc.). And on the plus side for Apple and its shareholders, it's another $499 essential.