Which year is my favorite? Only one? That's certainly a tough one, but 2007 has my heart. Kind of like you timoth, it was the first year I started to really collect Lego sets. Sure, I was given a set here and there, I really liked the three direct-to-home-video movies that had come, and I loved playing all the games on Lego.com. But 2007 was the year that had some of the best themes, sets, and website games.
It was also when I started to really get into the stories of the Lego themes. Spent countless hours researching every Lego product line that had come and gone, learning all of the story, the history and significance of the sets and new pieces in them, etc.
I do find it funny that my favorite year of Bionicle had an underwater theming to it, as my favorite System line also comes from this year, Aqua Raiders. Yeah, the story and characters are bare bones, the sets haven't aged all too well, but it's still my favorite System theme. Though it wasn't the only remarkable System theme at the time, 2007 Castle is my favorite year/line of the Castle series, with Knights Kingdoms II not far behind. Mars Mission, my brother's favorite theme and one I also hold in high regard came out that year. Exo-Force was around, all in all, it's the year I have the most nostalgia for and to me Lego has failed to really capture that same feeling since.
Sure, there have been a couple of good short lived themes that liked about as much as those in 2007, like Power Miners and Heroica. For me, Ultra Agents has been the only theme to really have captured that same spirit I felt in 2007. That theme had the same magic that Alpha Team did, which Agents failed to replicate.