Not sure if I even know what's underrated or not, considering I'm not really active in any star trek communities these days, but I'll just base these on how often I hear about them and if I've ever really had must discussion with them in the past.
TOS: I've always really loved the episode "The Conscience of the King" and I never hear anyone talking about it, really. I thought it was a decent mystery and, albeit maybe its because I was young when I first saw it, I didn't really see the plot twist of who the killer was coming. I thought the acting from Shatner, Arnold Moss (Kudos), Bruce Hyde (Riley), and Barbara Anderson (Lenore) was very good. It pretty seriously tackled some dark shit as well. Massively ballsy move on Star Trek's part to show a pretty nuanced look at the psychology of a dictator a mere 20 years after the end of WWII. I also think it's so interesting to give Kirk that piece of backstory and I find it a shame that it was pretty much retconned by never being mentioned again (at least, never that I can recall)
TNG: The season 3 episode "The Survivors" is a favorite of mine that, again, I don't hear talked about much. It's very scifi, the idea that an omnipotent, Q-like being could fall for a mortal and what would happen if that mortal was killed and someone with that much power for revenge was given the reason to take it. I like that, in the end, Picard takes pity on him.
I also always really liked the episode "The Bonding." As someone who not too long ago went through a period of grief, that episode does an excellent job exploring a lot of those feelings and how people with similar trauma can trauma bond. It also proves that Worf is actually the most shittiest person to have as a family member, considering he fights the entire episode to get Jeremy to be his brother and then we never see Jeremy again.
DS9: I always liked "A Man Alone." There's a lot of small gems in the earlier seasons that I feel get overlooked because the earlier seasons of most Star Trek shows are pretty rocky. But I think if I had to choose one, I'd say that one. It's been a while since I did a DS9 rewatch, so I'm not gonna talk in depth... but yeah. I like that one. And never hear about it.
VOY: I can't remember the name of it, but that one episode where Janeway "dies." I know that episode tends to be a hit with people who ship Janeway and Chakotay, but even outside of that I always enjoyed that episode. Again, a very scifi plot. The edition of Janeway's "Dad" showing up is pretty fun too.
Also, always loved the episode "The Raven." However, I very well may be biased as Seven is one of my all-time favorite Trek characters and any episode that dives into her backstory is going to be a hit with me. That episode makes me weep though. Little Annika deserved better. Literally fuck her parents.
Oh! I wasn't gonna list three for Voyager, but here we are. They keep popping into my brain. The episode (again, cannot remember the name) where they find Icheb's family I always really enjoy when it comes along during my rewatches.
Enterprise and onward I'm less familiar with so I don't feel I can really comment on them lol.
Remember Me... goddamn I forgot how much I love that episode!