There's quite a few actually:
First is The Way To Eden. I was always somewhat embarrassed by this episode because all I could see were the "space hippies". Watching it now, I can see discern the plot that was there all along; that Sevrin was a manipulative and older person preying on the idealism of the young to achieve his own wishes. Even better, I actually like the songs now as well which don't sound nearly as hackneyed as I remembered and give the episode a interesting change of pace.
A few others, like The Lights Of Zetar and Spectre Of The Gun play better to me now that I'm an adult than they did when I was a kid. I thought it was kind of goofy for Scotty to fall so hard for Mira Romaine but now find the in-story rationale behind the romance and it's portrayal quite sweet. I was never a fan of westerns so Spectre Of The Gun didn't do much for me as a kid but now I consider it to be one of my favorite episodes for various reasons.
Finally, I'd be remiss if I didn't mention Star Trek:The Motion Picture which I found difficult to watch for many years. It wasn't until the BluRay disc came out that I suddenly could watch the movie and divorce myself from all the disappointments I felt back in 1980 and think that they changed everything. Now I consider it to be my favorite Trek film. It's not perfect but I find myself watching more than nearly any other Trek film made.