I'm with Bartrim here. I love the second half of season 2. It's the highpoint of the series imo. Like Loophole, the Key to Vector Sigma was my favourite though hands down though I have to disagree that the Aerialbots are the best.
I liked a lot of Season 3 too now that I'm older. I watched a bit of it but it was never the same till I got older and appreciated the more sci-fi feel of the series. I mean I did have some faves but as a kid it was kinda painful wathcing Prime die again in Dark Awakening.
Though the Return of Optimus Prime was a pretty damn cool story. I remember smiling w/ glee as a I watched that. I was only annoyed they didn't play more of the Touch but as a youth, it was an awesome moment to see Prime return.