I find it exceedingly hard to pick a favourite, as pretty much each and every one of them blew me away during my first playthrough.
If I was forced to take a pick, I'd probably say... hmmm... yeah, they really all are memorable for quite different reasons.
I think even though it was 'very easy' compared to some of the other, more insta-death ones, the Sif boss battle would have to be my special favourite number one one. I've been fighting deadly shrubbery, little and giant mushroom folks with strange otherworldly chants on their lips, died to invaders and teams of cheating, exploit-exploiting smurfs, when I first noticed that Alien-looking vertical line of light from afar. I didn't know what it was at first, and the first time I crossed that bridge yet another invader was announced to me. So I took up position right under the giant gate, watching the bridge. The glowing red invader soon popped up from out of the woodwork, and he seemed... pretty determined and quite scary. I didn't feel like putting up with him, so I ran through the gate and... nothing happened. I ran around the area and... nothing happened. When I thought the game glitched out on me, or I did something wrong, or maybe I missed something, I closed in on the tombstone and triggered the cutscene - woah. What the... Just the sight of a giant Okami-style faithful dog creature blew me away, and that was even before the great grey wolf snatched up the sword and came running at me.
The moment I reduced Sif to a hobble, I really didn't feel like killing him. The moment I did was a pretty intense rush of mixed emotions. I was glad I was victorious, but I felt really, really pissed about having had to kill that creature. I had to quit the game and pause for a while.
But I really have to say it again - every boss fight is pretty well set up and impressive in its own right. The rush of the first encounter with the Minotaur demon, the first time you make it to the roof of the chapel, the first time you meet Queelag, the first time you enter Mr. Deadly Blind Dragon's cave, the first time you get killed half a dozen times or so by Ornstein & Smack-a-Hero... it's all good in my books. And it made so many AAA title rides pale in comparison.
With the DLC, I was amazed, impressed and just plain stunned by the Manticore encounter. What a way to roll out the unwelcome mat. Major kudos to From for that one, ballsy move that's consistent with what I got out of Dark Souls up to that point.
If we include the DLC in this vote, I think I would have to go with not-so holy anymore Knight Artorias. He's quite the wicked one, isn't he. I screamed out in agony and amazement at his various surprise moves. He's pretty much 100% pure nightmare material. I wonder what he was like before the Abyss took him and he... turned. Hey! That's actually an origin or prequel material story I'd give a flying melonfarming farm about - The Adventures of the holy knight Artorias, from the moment he picked up his sword to his untimely demise. As long as it's not handled by George Lucas, not written by anyone working for the Bioware Brothel Softcore Porn Gang and not including any Jar Jar Binks, I think that would actually be something awesomely good.
Awesome, awesome 'game'. I found it to be quite inspiring and metaphysically challenging at times, nothing like any other game I've played... ever.