Just if anyone missed the Independet Tour from the Wolfire guys: Part 4 : Aquaria with some making of stuff 
(hopefully Alec&Derek inlcude a "large/full" Making off Special to the boxed Version of Aquaria)
Thanks for that. I found the World of Goo one very interesting when I found it a few weeks back, didn't realise they'd done several more.
As a note to mentioning the puzzles being hard: Watch the World of Goo one, you'll note that it's pointed out how the game subtley explains how things are done. Aquaria doesn't do this.
It's not a criticism imo, and the guy doing the video does point out it's a design decision. The reason I bring up World of Goo is because that skirts around explaining things, which Aquaria does at the beginning then largely leaves you to find things in the background or such that aren't immediately obvious.
Finding the right spot for that sort of design in a game as complicated as Aquaria is far FAR harder than a comparitively simplistic one such as World of Goo, but the point being made in the video is that for a lot of people it was too far on the "obscure" side of the line, and as such it is deemed as hard.
Personally I can't believe people got stuck at the door mentioned... It was really obvious to me what to do there.