There are a couple of games which kicked my ass as a kid, but found fairly easy in later years.
Commander Keen: Episode 1
Did you know you can kill Vorticons with the ray gun? I sure as hell didn't! God that would have made it easier.
Star Trek Voyager: Elite Force
When I was a kid I simply couldn't beat the final boss, despite my many attempts. I almost suspect he was made easier by an update I must've downloaded when I reinstalled it a little while back. I can hardly believe I found that so challenging.
Evil Islands (game I doubt anyone here has ever heard of)
When I realized that actually taking party members with you is the best way to gimp yourself, since you eventually have to leave them behind and get new ones. All they do is steal your experience.
Warcraft III
I found the campaign very challenging when it first came out, but when I replayed it, I breezed through it easily.