2007 was my absolute favorite, despite having been around since 2001. I loved the underwater theme, and the story felt dark and mature without being needlessly edgy. The Barraki were great villains made greater by their collective backstory, and the struggles of the Toa Mahri were treated with a proper sense of gravity without being overwrought. Plus, Hahli the Barbarian.
2005 is my runner-up year; I know this is going to be an unpopular opinion, but I really did like Vakama's character development. Could it have been handled better? Definitely. But it could have been a lot worse, too, and it all payed off brilliantly in Time Trap. Plus, Roodaka introduced us to the Vortixx race, and the Visorak were pretty cool, too.
2008 is my third favorite. It took me a long time to warm up to a lot of the revelations recieved there, such as the Toa Mata's history, the Makuta as a race, and the GSR itself, but now that I have, I can honestly say that it was a truly spectacular year and a properly climactic ending to the first overall story arc of the franchise.
As far as least favorite years go, these three are simply the ones I love slightly less than the others; they still had plenty of strong points in their favor.
2006: I know a lot of people love this year, but it personally feels to me like the very antithesis of everything that made 2007 brilliant. The villains were the worst sort of blend of overly-grimdark (slavery, man!) and cartoonish, what with their blatant evilness and constantly backstabbing one another. The designs were all ugly (save for Brutaka) and the story just constantly insisted on being dark for the sake of being dark, without any real depth or purpose. Still, I liked Matoro's development, and Zaktan on his own was a good antagonist.
2009: The concepts were great. In the comics, the Skrall were badasses and Tuma actually had some small bit of depth to him. However, the execution was largely lacking, and nowhere more so than in The Legend Reborn, which sadly stands as the main representative piece of media for the year. I wished the Agori could have been a bit more alien in terms of their culture and values, and Mata-Nui seemed somewhat bland (though having Worf's voice helped abate that somewhat) given he'd been forced into a mortal form and exiled from his old body, not to mention that the billions of beings he was responsible for facing all sorts of horrors at Teridax's hands. Not even a little bit of emotion?
On the other hand, I liked the desert theme, and again, the comics' depiction of the Skrall was a lot more favorable than they're usually remembered for.
2010: Stars were underwhelming, golden armour came out of nowhere, the climactic battle felt as rushed as it actually was, and without further story to lead up to it, felt rather abrupt as well. Also, mooning Teridax still makes me go "wat."