(I recently re-started FFVIII and found the Squall/Zell dynamic quite compelling, but didn't play enough of it to confidently give an opinion on how I'd write the pairing myself. That said, Squall kissing Zell to shut him up feels fun to me)

As for a story that's etched into my soul, I of course must say Fullmetal Alchemist (the manga, not the animes). Ed's journey to fix his past mistakes is very personal to me, and is mirrored by Roy's journey to do the same. The themes of hubris, friendship, and moving on just hit home for me in ways other series haven't.