1. Catalysts: Green Goblin was introduced and was badass, but more importantly the development of Peter's relationship with the supporting cast, Harry starting to succumb to drugs, questioning Harry's coupability as GG and the awesome intro to MJ most of all made this the best for me.
2. Natural Selection: Lizard rocked. Maybe not as good as Night of the Lizard, but the action was better and it was the one episode besides Group Therapy that I felt Spidey was really getting his ass kicked. I mean he was pushed to the edge and worked well with Brock and the Lizard deciding to try to eat Billy instead of succumbing to reason. Best of all was the finale that featured Peter making a really stupid mistake and losing his job as well as the respect of the Conners family and Brock in the process. The last moment with Peter considering quitting was awesome.
3. The Uncertainty Principle: The dialouge between Spidey and Tombstone was awesome and the surprise ending of Harry being the GG with the possibility of Norman being an even worse ass hole than in the comics (as Lee originally conceived) or the movies was really interesting. Plus more great supporting cast interaction.
4. Intervention: The retelling of the origin was poignant and memorable as opposed to contrived and boring like in TAS. The mixture of movie and AF#15 worked perfectly and the reuse of the previous episodes to recreate the cover of ASM #100 was appreciated. Uncle Ben rocked in this episode and seeing Dark Peter was nice.
5. Group Therapy: I'm admittedly not a big fan of the Sinister Six concept, but it worked nicely here. Doc Ock was much cooler in this episode andi t had probably the best action of the season. Intense fighting and a nice subplot of Peter not being there for his aunt after she had a heart attack. But it was mostly an action driven episode.
6. Persona: I like BC, what can I say? She was good in this episode all the innuendos and sex jokes were amusing in a kids show, but moreso was their interaction and the ability to see Cap. Stacy as a trusting ally of Spidey. The noddds to the movie with the black suit and upside down kiss were also appreciated.
7. Reaction: Doc Ock becomes a badass. What can I say? I still think TAS's voice for Doc Ock and origin were much better, nor did I like this Doc Ock having a battery life, but the action was amazingly good. And seeing Liz Allen break up with Flash Thompson over Peter Parker was hilariously cool to me as was all the supporting cast interaction.
8. The Invisible Hand: Maybe the most well rounded episode. Spidey fights a b-lister in Rhino. But Rhino tears up the Daily Bugle really badly and Peter has to use his wits to beat him. What is more interesting about this episode is how this is where the show really picks up and all the pieces come together. Notice all but one of the above episodes on my list are after this one. It is in this episode that Spidey meets Tombstone and gets his ass kicked by him. The dynamics of the show change drastically. Also, Aunt May coming to the Bugle and guilt tripping Betty out of going to Peter's prom with him was classic. It made this Aunt May above the cloth of the comics or TAS. Still I prefer Rosemary Harris's portrayal of the character the best. And the ending with MJ. Classic.
Those I felt were the absolute best top notch episodes. The others were good, but these were great.