I tried my hand at this through a process of elimination:
1. The End of This Chapter
Such a whirlwind (no pun intended) of emotions, both musically and lyrically: while there are some brief grunts and double bass drumming at the end, it also manages to maintain this melancholy, ballady feeling throughout its duration, and I've never really heard another song like it by anyone. While Caleb obviously is an obsessed and deranged person, he also comes across as human and you can't help but feel a little sad and sorry for him, so the lyrics hit a nerve that few other songs can. Goddammit Tony, stop manipulating my emotions
2. The Power of One
While TPOO is not my personal #1, I would say it's the definitive SA song that sums up their whole range of styles. The lyrics are really good, speaking of which I should read the book they're based on someday.
3. White Pearl, Black Oceans
WPBO remains the peak of Tony's musical and lyrical storytelling, and it's so epic you could even imagine it as a full-length movie.
4. Caleb
A nice villain origin story, and I love how the song gets progressively heavier, until it suddenly calms down again at the end - once again the music and lyrics complement each other perfectly.
5. It Won't Fade
A kickass heavy tune that I'd love to hear live (feel free to use my idea of a show including all the wolf songs, guys!), though I doubt it'll return now that Tony and Jani are on good terms again. Nevertheless, I love the raw and real emotion in this song.
6. My Land
Such a simple but timeless melody that's fun to sing along to live, and the atmosphere is incredible. This could easily replace FullMoon as the token song from Ecliptica in the setlist IMO.
7. Replica
According to the official SA book people would sit down during Replica when they played it in some of the countries that had been through the Yugoslav Wars in the 90s, which says a lot about how much it's resonated with fans. It's dear to me as well, as it reminds me of my late grandfather, who fought in WW2 and lost his brothers there.
8. Draw Me
Another ballad that hits you right in the feels, particularly when you know
the story behind the lyrics. "I must have... faaaailed" is one of Tony's top vocal moments, particularly in the Live in Finland version.
9. Don't Say a Word
I know they've played it a million times live, but DSAW is such an anthem that never gets old - that chorus is just massive, and Jani's solo is one of his best.
10. To Create a Warlike Feel
I had a hard time deciding between this and The Boy..., but the bit where Tony is singing in English and Jarkko Martikainen in Finnish is so epic and "stripmine your private road to hell" is such a badass lyric that I couldn't leave this out.
I realize there's nothing from TDOG in there, even though it's one of my favorite albums, but The Truth is Out There almost made it. While making this list I noticed that I don't rate some of the quirkier and more chaotic mid-era songs like The Dead Skin and Fly with the Black Swan as highly as I used to, even though I still really like them - it's just that my taste has changed over time.