IMO, The End was the freakiest boss in the game...so damn frightening, you try your best not to make any noise and stay hidden.. I had a hard time beating him, but its a big relief once its done. Really cool boss. Better than sniper Wolf.
MGS3 = great game.

I had a little trouble beating The End, only because I kept getting lost and losing track of his footprints trail. Once I started relentlessly following him around, though, it wasn't too hard. Just keep popping him with the traq gun and eventually he'll pass out.