This is an incredibly difficult question, as there have been a number of years I can look back on and think that visits then were the best ever.
However, I would rule out 2002-2006 entirely, as I generally think that period was the weakest in my Alton Towers visiting history - mainly as the new attractions were overall not as good as they could have been, and entertainment was steadily reduced.
Thankfully, times are changing again - and I feel that since the end of 2006/start of 2007, the park has been improving.
For me, I would say that the 2007 season was pretty good, mainly because the park brought back a Halloween event which, whilst it could have been better, I enjoyed an awful lot. The 1997 season I remember visiting, when Ripsaw was new, was magical. I remember visiting, vaguely, when RMT and Haunted House were new in 1992 and being wowed off my socks.
It's really hard to day in all honesty, but it would have to be early to mid 1990's for me when Alton Towers was coming into its own.
After a few bad years in my eyes, I am hoping though that come the next big thing (hopefully 2010) - we'll be choosing that as the best year.
For now though, 1997. There was some buzz.