Now, I'm aware that there's a considerable portion of the "Buffy" fan base that likes to pretend these comics didn't exist because they disagree with certain decisions made in the storytelling, and those people probably aren't going to like my list either. But they happened, they're part of "Buffy" canon, and I think with time, we'll come to love them (well, SOME of them) as much as we love the great moments from the TV series.
Rather than try and rank them, I've presented them in chronological order, with a link to my review of the issue when available.
Oh, and obviously spoilers within for those who haven't read the entire run.
1. Buffy jumps out of a helicopter - Issue #1, Pages 2-3
This was the first image from the series, not counting the 1/3 page that came before it, and it definitely set the tone that this was going to be a different kind of "Buffy". I remember when this was released before the issue, and Buffy fans started freaking out because Buffy was jumping out of a helicopter and holding a gun. Some fans are still freaking out about that -- and various other things in Season 8 -- to this day.
2. "Buffy" dies - Issue #5, Page 22
Really it's the whole issue, in which we meet one of Buffy's decoys, and get the story of "her" life and death, without ever learning who she is. But the last splash page, with her dead body against the blank white background, is just visually striking.
3. Faith kills Genevieve - Issue #9, Pages 12-13
4. Buffy's first confrontation with Twilight - Issue #11, Page 14
5. Buffy sleeps with Satsu - Issue #12, Page 4
6. Buffy kills Willow - Issue #19, Page 22
7. Buffy the Animated Series finally comes to life - Issue #20, Page 5
8. Buffy flies - Issue #30, Page 22
9. Angel is Twilight - Issue #33, Page 14
10. "The Porn Issue" - Issue #34
11. Twilight/Angel kills Giles - Issue #39, Page 16
As you've probably noticed, the moments are pretty condensed to the beginning and end of the season. Five come in the first 12 issues, and four more come in the last 11. I think that goes to show that the complaint about Season 8 being too long -- 40 issues stretched out over nearly four years -- was a valid one. Of course, Dark Horse has already listened, saying Season 9 will be just 25 issues.