Such a simple and seemingly obvious idea, but many teachers skip this step. Then, the stars aligned and my boss sent me a link to a great FREE tool she came across today: eduCanon. eduCanon lets you embed multiple choice questions into the timeline of a video and collect response data! You can even provide answer feedback to students right then and there. How's that for flipping fantastic? Other options include inserting free-response questions (available with the paid version), web content, images, equation editors, audio and more. Best of all, you can prevent students from skipping past parts they haven't viewed yet!
What a powerful tool for flipping instruction, or for use in a blended learning environment! If you try it out with your students, I'd love to hear your thoughts!
EDIT: Someone responded in the comments that they liked EDpuzzle better than eduCanon. I hadn't heard of it before, so I checked it out. I have to say EDpuzzle is pretty awesome too! I like that you can import videos from several sources, and their customer support is awesome. I couldn't figure out how to edit questions after they'd been created, and they responded within a few hours AND immediately implemented a functional change that I suggested, making it much easier to edit existing questions!