The use of "100%" in your sentences is understandable, but it can sound a bit awkward or unnatural. Here's how they could be improved to sound more natural:
1. Are you 100% sure? (This is the most natural and commonly used phrasing.)
2. He looks 100% like Tom Cruise to me. (This sounds more natural for the context you're describing, where the person resembles Tom Cruise but isn't actually him.)
3. Do you 100% agree? or Do you agree completely? (Both options are correct, but using "completely" can sometimes sound more natural.)
In everyday English, "100%" is often used for emphasis, but it's usually placed before or after an adjective (e.g., 100% sure, 100% agree) rather than in random positions within the sentence.