Hmm, I had to think on this.
For my favorite Monster I'd have to go with Tonberries. Nothing else I've ever seen has stricken me as so cute and yet so horrifying.
Now, originally I would have said that Kefka was my favorite villain, but after thinking on it a while I decided that, while Kefka will always be my favorite madman, Genesis is my favorite villain. For a good number of reasons too. For one, he's actually a genuinely likeable fellow. Genesis is the kind of guy you'd probably hang out with (or have depending on your clicke). Also, he isn't evil in the least. In Crisis Core his main motivation is trying to stand up to the real evil and try to save himself in the process. Which brings me to my third point, even with CC under our belts, we still know little about him. He's still a mystery and really the only reason the Compilation of FFVII is incomplete.
There's a;so that other thing...what was it....oh, yeah! His character is based on Gackt Kamui. The single greatest Japanese musician I've ever heard. (Incidently, Tebian, I noticed there's not very much Gackt in the request catalogue...just saying)
Now, my favorite Boss ever is Gilgamesh. I could go on about it but I'll let the videos talk for me.