My favourite encounters/concepts:
1) The Collossus sequence in Gate Pass in #9.
2) The "game" with Flight in #10/the tornado/hailstorm/firecloud obstacle course. IMO best combined together into one encounter. Don't let it drag on by making the mistake of letting Flight pick up the ribbon as a minor action like the players can (I did that by mistake, makes the encounter too long).
3) The chase sequence after Rhuarc in #7.
4) The whole of the first adventure. I just adore it. I'll go on record as saying that, all bias aside, I honestly believe it's one of the best adventures I've ever had the pleasure to run in 30 years. I am the publisher, though, so take that as you will. The way it imparts info to the players without boring them, the way they feel they are making important decisions (despite it honestly being fairly linear), its ability to immerse a new group in a new setting and plot quickly and have them feel invested in that plot while making a new city feel alive and familiar all in the first session is so well done. I take my hat off to Ryan.
5) The Tempest. It's just so evocative and awesome and cool.
6) The concept of the burning forest, although I'd agree with criticism that that's the most linear adventure.
7) The halfling rivals in #6, and why, oh why, did I skimp over them when I ran it? Why didn't I run a one-shot where the players played the halflings? I utterly failed with the halflings and regret it.
8) The idea of the Inquisitors, although in my own game I made them much more potently anti-magic than as-written. But that's just a preference.