http://progressiveboink.com/archive/teamrocket.htm I don't agree with everything this guy says, but he managed to pick up some things I missed, so I'm gonna copy-paste the stuff that I didn't notice before that caught my interest and italicize the revelent bits.
Episode: 3. Ash Catches a Pokémon!
The context: In their first appearance, the Rockets, along with Koffing and Ekans (God rest their souls), looked like A-1 bad asses. So in this first official attempt to capture Pikachu in the woods, it's fitting that Team Rocket AND their two best Pokémon lose badly to one of the smallest and weakest Pokémon around. Caterpie, with all the strength and reserve of a green turd, uses weak attacks and completely dominates. It was the first time we could see how pathetic these guys really are.
The bizarre thing: Before this, Team Rocket's "plan of attack" was to fly over the Pokémon center and drop bombs in it. Pretty effective, right? After this, Team Rocket's "plan of attack" was to build a big robot that would dig a hole, and then they could dress up like hula girls or something and try to get Ash to fall into the hole. Caterpie must've given them brain damage.
(I'm guessing that an executive complained or something and that that's what led to the change in Rocket effectiveness. Still of interest, though. Remember, kids, 4Kids is not the cause of all censorship!)
Episode: 14. Electric Shock Showdown
The context: Another well-known entertainment site covered this episode, the big Pikachu vs. Raichu battle for the Thunder Badge, and COMPLETELY omitted the best and most significant part of the episode. Moved by Pikachu's bravery, Team Rocket debuts their "conscience" by dressing up as cheerleaders and rooting for the yellow rat-that-looks-more-like-a-rabbit. The Rocket cheerleaders appear many more times during the run of the show, and the "conscience" plays a big part in their famed rise to "face" glory in Pokémon the Movie 2000.
(Interestingly, this is also the episode where at the end the narrator talks about team rocket almost as if they were co-heroes. Is this where the redeption arc (that's usually reserved for shounen rivals like Sasuke or Kaiba but not in pokemon because Gary is basically Ash already and therefore not really a proper shounen rival anyways) started?)
Episode: 45: Holy Matrimony!
The context: Ah, controversy. The ending to "Holy Matrimony" gave one group of Pokémon fans an endless supply of fan-fiction material, while giving the other half reason to jam their index finger down their throat and vomit all over the television. Reassuring their partnership and friendship, Jessie and James fly away in the Meowth balloon, hands clasped. I ranked this number one because it's one of the ONLY Team Rocket happy endings, and because we didn't have to sit through another video package telling us how much Ash loves Pikachu. We GET it, okay? He has sex with the mouse, now stop ramming it down our throats.
(This, after an entire episode where Jessie and Meowth abuse James and use him for money? This isn't love, people. This is some form of Stockholm Syndrome. There is no way these people's attatchment to each other is healthy or natural. Once you look at the full context, this single "happy ending" becomes greatly disturbing.)
Episode: Special Ep: Snow Way Out!
The context: Cold, hungry, and lost on a big snowy mountain, James and Meowth bemoan their situation...until Jessie reveals her fondness for snow. When questioned, Jessie reveals that since she "didn't have much growing up," her mother would make her entire meals out of snow. Snow rolls with soy sauce, snow pudding, the works. This moment helps move Team Rocket from "weird" to "psychologically damaged."
(The only reason I don't talk as much about Jessie being messed up as much as James is, well, he gets a whole episode about how his past screwed him over and Jessie's pre-James backstory is sparse and scattered across pokemon canon. Heck, other than here, the only things we know about her mother are on the CD Dramas. Jessie's mom, according to the CD dramas, was a high-level Team Rocket agent who was looking for Mew and disapeared. Judging from the fact that Jessies' mom apparently fed her daughter snow when she was alive... okay, Bulbapedia tells me that Jessie's mom put her daughter up for adoption before she dissapeared and that that's when Jessie was forced to eat snow, and I'm not sure who to believe here, but the fact that Jessie EVER had to eat snow for food shows what a horrible fucked-up life she must have had as a kid. Not only would it have caused enormous emotional trauma, it would have probably led to her being malnurished and physically ill as well.)
Now don't you feel really, really bad for Team Rocket? I mean really bad?