The Archfiends for sure, but Scarmiliogne and Rubicant are easily my favorite. The showdown with all four of them is also a nice highlight. I also love the one legitimate fight you get with Golbez. My other favorites are all the summon battles since they all have a bit of a puzzle element to it and I love the idea of reflecting Megaflare back at Bahamut. Honestly, FFIV has a lot of great boss battles.