It's impossible not to have Safer-Sephiroth (or Seraph-Sephiroth if we believe the mistranslation fan theory) on this list somewhere. He's legendary, a member of the Ivy League of boss battle alumni along with Jubileus from Bayonetta, Liquid Ocelot in Metal Gear Solid 4, and those ducks that Warren Robinett claims are dragons from Adventure.
There's nothing I can tell you about Safer-Sephiroth that you don't already know. He looks like Tetsuo by way of Angel's Egg and can hurt you with a short film Supernova. One-Winged Angel is one of the most recognizable songs in video game history, and it was the first Final Fantasy song to include vocals.
While some people might say that Safer-Sephiroth has lost some bite so many years later, I disagree. The buildup to this fight is excellent -- you've spent all this time grasping at Jenova's clones, and then, when you finally come face to face with the man himself, you aren't shown a radiant, heavenly beauty but are instead confronted with a twisted quasi deity crafted out of jagged polygons. It's haunting, but you're unable to look away.