3>5>4>1>2
I didn't like 2 that much - it felt like the locations were largely boring (a bunch of tiny, empty islands, a mermaid village that consisted of about 3 screens, and a relatively empty jungle island), and the episode had the most blatent model reuse of any of the episodes (one merfolk model and about two pirate models, aside from the main cast.. that's kind of lame). And overall the puzzles weren't that interesting (and I still don't get why I had to throw the melted gold off the cliff vs. just walking up to the model, seemed unintuative). Add in bad audio compression problems (which were fixed, but did exist when I played it), and that's why it goes to the end for me. I will give them credit for the "USE ___ WITH ___" jokes
I felt 3 was all around the most balanced - excellent locations, clever puzzles, great plot, and of course, the best end credits of any episode!
4 & 5 are very close, but 5 wins out slightly for being the conclusion and just having an awesome story.
1 wasn't actually that bad, but it felt very basic. That's ok because it had to introduce everything, but overall it felt very traditional vs. some of the cool stuff done in future episodes.