There truly are too many good ones to list.
I've watched them all at least several times and I'd break it down like this:
50 Excellent episodes
50 very good episodes
50 good episodes
20-25 mediocre episodes
5-10 bad episodes
A few that stand out:
The Pony Remark - Not only is this one of the best pre-"Super Jerry" episodes it also introduces two fundamental supporting actors: Len Lesser and Barney Martin. It shows Jerry for what he truly is, an overgrown kid desperately needing to be the center of attention no matter who he steps on. And I love Manya. She dominates the memory of the episode she completely that it's easy to forget she only appears in one scene with just a few lines. This is also the episode where Michael Richards begins to hint at the character's potential. Levels, Jerry. Levels.
The Apartment - a perfect encapsulation of something we've all felt. Who among us hasn't patted themselves on the back to celebrate saintlike nobility only to regret it deeply very soon afterwards? Not the most lol funny episode, but one of the best written early ones. Perfectly story arc. Not to mention it prominently features an openly gay couple in what, 1990?
The Heart attack - introduced the star turn guest appearance. Stephen Tobolowsky is lol funny as the faith healer. I know some might point back to Tierney as Elaine's dad, but for me this is where it really began.
The Serenity Now - As others have mentioned, one of the funniest episodes in the series. It also dabbles in the surreal very effectively. Hoochiemama!
The Summer of George - To me it's one of most fun to watch, effortlessly tying together its various plot lines. ......Shadow!
The Doodle - it's so rich in content it feels longer than 1/2 hour.
The Contest - catapulted Seinfeld to the level of Super Series. They never say the word masturbation once.
Worst episode? Let's not count "The Smelly Car"; not really an episode, rather some sort of weird experiment wrong. Probably a reaction to the fact that Seinfeld received much criticism for having Jerry drive a BMW.
My pick would be "The Visa" - The worst Super-Jerry episode. Its starts with a premise too flimsy even for a sit-com: that Jerry can't not be funny, and that it drives neurotic George crazy. The whole visa thing is pretty ridiculous for those of us who have dealt with this types of issues. It doesn't work like that.
Best guest appearance - Bookman. If you look closely you can see Jerry trying hard not to crack up during their scenes.
honorable mention scenes:
Mel Torme singing to "retarded" Kramer. If that's not one of the funniest things ever put on TV I don't know what is.
The sax player trying to play after performing oral sex on Elaine. Who knew she was poison down there?