You‘ve listed a lot of “Best” categories (“Most fun encounters etc”) and I appreciate mega dungeons can just be explore, kill, loot but which ones would you say have the Best Story or Overarching plot?
Of those listed, I've only run Ruins of Undermountain and Rappan Athuk. It still amazes me that some of the parts of the maps for Undermountain are taken from the maps of other modules. Not on the list, I've run Temple of Elemental Evil (albeit a long time ago).
To answer the question you posed, I've played in ToEE, some of Rappan Athuk, and most of The Vault of Larrin Karr (which you didn't list, although it isn't "mega" per se). I've read Lost City of Barakus, Tomb of Abysthor, and a host of others.
My favorite mega-dungeons are those that have context, and especially ones that have a surrounding sandbox region that brings the dungeon to life. I like mega-dungeons that make some kind of sense in the world.
I also like mega-dungeons that give the players a break and allows them to "come up for air" so to speak.
Highfell and Archaia aren't on the list as far as i can tell.
I've been running Rappan Atthuk for a little over a year. Love it, but it will be one of my longest campaigns and once done, I'll probably be done with megadungeons for a while.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.