Well, of course this is all highly subjective... There have been some "hurt/heal" threads run that reveal how much TBBS members like the episodes. I found myself in agreement with a good many, but not all.
If you judge TOS episodes against the later Star Trek series, you're penalizing it unfairly. The late 1960's was a very different time, in terms of episodic TV maturity and availability of technology. When stacking up TOS to what was out in its day, it really shines. Unfortunately, there are some dismal episodes. Some need to be taken as a kind of farce or comedy in order to be enjoyed, but some can't even be saved with that... I find "And The Children Shall Lead" a contemptible episode fraught with just ridiculous premises and bad acting.
"The Menagerie" had some slow parts to it, but I wouldn't call it boring at all. I found it very imaginative how "The Cage" was reused. Of course, the whole misleading behavior of Spock was so out of character, that it was hard to believe. Plus, making Commodore Mendez an illusion was unnecessary, as well as peculiar (maybe they just wanted to make it seem like less was real). But overall, the story worked really well. It's not in my top 5, but it's in the top 10 for me.
I think "City On The Edge of Forever" was ingeniously crafted, despite the myriad of changes from the original story and the inherent issues with time travel. A very colorful departure from what Star Trek normally produced. If you hate 1930's sets, I could see how you'd find it dull as much of the episode is like an old time movie.
The Enterprise Incident certainly had some conceptual problems, but I liked what they were trying to do with it. It was really great seeing the Romulans again. It's in my top 10.
"A Piece of the Action" was half-comedy. Yeah, it had its silly moments, but overall it touched on an entertaining idea and I definitely wouldn't say it's "unwwatchable." True, I think the Iotians being as intelligent as they are would learn from "the book" but not copy it outright. The behavior harkened back to a very primitive time in American culture, something I'd expect the Iotians to improve upon. However, given what they did with the technology at hand, I'm surprised Spock would even suggest that they'd be capable of figuring out the key transtator mechanism, being "the basis for every important piece of equipment that we have".
"Space Seed" in of itself was not very interesting to me, once we got past the first 20 minutes. Khan's take-over of the ship wasn't very well planned, given his "superior intellect". Also, there wasn't enough time for his crew to get educated on Federation technology to make them useful outside of just brute force. Ideally, it should have been a 2 part episode. In the 2nd half, Khan exercises a cleverly crafted plan to take over the Enterprise, utilizing much more inventive ways to secure the ship. It would have been great to see a scene with a huge number of the crew crammed into the shuttle bay. Anyway, they missed an opportunity in the remastering to insert a brief scene of Chekov, to help clear up the mistake in TWOK. This episode is not in my top 5, but what makes it enjoyable is how TWOK was built upon it.