Yes, there are a bunch I haven't seen. I'm really late to
"Star Trek" as I only started watching it last year (though I've been watching TNG since childhood). I never bought the DVDs and when I started watching re-runs on TV, I couldn't commit to watching it every day due to laziness or other commitments, so I missed several episodes in every season.
By the time I got to season 3, I was getting annoyed with the show and purposely skipped a few episodes out of frustration. I was thinking of maybe starting a poll to ask which episodes people would most strongly recommend of ones I haven't seen yet, but I guess here is as good a place as any to ask. I liked a few season 3 episodes, but the episodes of it that I didn't like soured me on the season so much that I don't have much desire to see the episodes I missed.
I am a little curious about
"The Way to Eden" based on what I heard about Spock in that episode, but generally I'd rather not bother with my gaps in season 3, so I'll just list the season 1 and 2 episodes I've missed.
Season 1
"Charlie X"
"What Are Little Girls Made Of?"
"The Galileo Seven"
"Court Martial"
"Arena" (I know about the Gorn because I've seen his fight with Kirk on Youtube, I've seen
"In A Mirror, Darkly", and it is popular as an action figure, but I have never seen the rest of the episode)
"The Alternative Factor"
"A Taste of Armageddon"
"Operation -- Annihilate!"
Season 2
"Catspaw"
"Who Mourns for Adonais?"
"The Doomsday Machine"
"The Changeling"
"The Apple"
"The Deadly Years"
"The Immunity Syndrome"
"Patterns of Force"
To each person, I ask which episode(s) would you most recommend and why? If I'm convinced enough that the episode is worth watching, I'll try to go out of my way to make sure I don't miss the episode the next time it's on the TV channel where I watch
"Star Trek".