My favorite years were 2004, 2006, and 2008, each for different reasons.
2004 was great because of the setting. Metru Nui was a detailed, bustling, crowded sci-fi/fantasy/superhero city that truly felt alive in the books, comics, and all other materials. I especially loved the rich worldbuilding that was done in the books (for example, the enigmatic references to Artakha, Karzahni, the Dark Hunters, and the Brotherhood of Makuta). 2004 revealed to us that an entire world beyond Mata Nui was out there, waiting to be discovered, and while it gave us tons of new information, it also raised pressing mysteries that haunted us for months (if not years).
2006 was great because of the characters. Voya Nui was a small-town sort of place (as you'd expect), and there were few enough characters involved for each of them to be fleshed out and focused on. Each of the Piraka had a very vibrant and entertaining personality, Axonn and Brutaka were epic, and the Resistance Team each had distinct quirks... and, of course, there was Vezon. 2006 introduced some of the most memorable and beloved BIONICLE characters, second only to the first three years.
Finally, 2008 was great because of the plot. After a steady escalation of drama and darkness from 2003 on, we saw the return of the good old Toa Nuva in a battle for the entire universe. And the battle didn't rage only in the main story -- 2008 was also the best year for serials. Federation of Fear provided not only a barrel of laughs, but also the mounting tensions for the Destiny War. And who could forget the MASSIVE revelations at the end of the year? 2008's plot had me on the edge of my seat all 12 months.
As an addendum: while it obviously can't compete with any of the above years, 2009 was my favorite year for sets. Sure, they lacked the complexity of the good old gear-and-axle days, but they made up for it by returning to BIONICLE's elemental roots in both colors and pieces. This was especially satisfying after 2008's sets, which were practically nothing but grey, black, and silver. In contrast to the Phantoka's and Mistika's nondescript blasters, the Agori and Glatorian wielded snowflake shields and ice axes, watery daggers and tridents, flaming claws and swords, leafy blades and vine-wrapped scythes, and so much more. All of which made the "eh" story that much more disappointing, of course, but the point still stands -- the sets were magnificent.