Movie-theater popcorn may be bad for you because of the oils it's popped in and the butter on top, but at least making it doesn't cause "popcorn lung" -- don't laugh, that's a real disease. It's also known as bronchiolitis obliterans.
Butter-flavored microwave popcorn doesn't really get its flavor from butter; it gets it from chemicals and flavoring agents. Diacetyl is what most people will point a finger at when they talk about how the health risks of microwave popcorn. Diacetyl is a butter-flavoring agent used in microwave popcorn -- by the end of the 2000s, some manufacturers banned its use in popcorn bags because of its respiratory risks (and, separately, a link to Alzheimer's disease), but you'll also find it giving a buttery flavor and smell to baked goods, candy and margarine.
Additional concern with microwave popcorn is what's in the bag -- aside from the popcorn. Without all the added chemicals, the popcorn would be an OK snack (high in carbs but low in fat – and a whole grain), but there are many chemicals coating the inside of the bag to keep the oils needed for popping from soaking through the paper, as well as chemicals to keep the bag from catching fire during the popping process. These chemicals also produce perfluorooctinoic acid (PFOA), which the EPA considers a likely carcinogen [source: Kotz]. Somehow, microwave popcorn doesn't smell so good anymore.
Want to DIY your microwave popcorn and skip the chemicals? Toss popcorn kernels in a brown paper bag, double fold the top of the bag, and pop as you would the processed stuff. You can also use a microwave-safe bowl with a plate on top to keep kernels contained as they pop.