Well, it's quite recent, but mine has to be Mewtwo in my SS.
Because of all the rumors of the "uncatchable Mewtwo", I was so freaked out when I finally decided to catch Mewtwo - except that I had used my master ball already! So I just thought "well, it's all or nothin" and I went into cerulean cave (is it right? correct me if wrong). After 30 mins of wandering, I finally found the purple humanoid of death. The first try catching it, my whole team got wiped out by it. The second try, I caught it with 3 ultra balls. I must say, I was quite pissed (thx pokemon handbook) that I was tricked for 10 years, but I think the fact that I got tricked makes this incident even more memorable.
Oh yeah, and that was my first Mewtwo. I had never seen his sprites, animations, moves, cry, etc. Probably one of the most important days of my personal pokemon history :)