A scare to remember, Advanced Battle (pikachu looses its memory and is tricked into joining team rocket!)
A corphish out of water, Advanced (ash's new corphish causes some problems, and TR also almost accidentally get themselves, may, max and brock killed)
Can't beat the Heat, Master Quest (Ash vs Gary in the Johto Leauge!)
Playing With Fire, Master Quest (Ash vs Harrison, johto leauge)
Ignorance is Blissey, Johto Journeys (Jessie meets a Blissey pokemon center worker who she befriended in the past, and it more than willingly helps TR steal the center's food..
Get the Show on the Road, Advanced (first hoenn episode, pikachu is sick with a fever that makes it delusional and uncontrollable and its at risk of....yes...exploding
. Also May totally fails at commanding her first pokemon attack, and there is a scene that mirrors the part in R/S/E where you chose your starter and stuff)
A Poached Ego, Advanced (shows how Team Rocket do sorta have hearts...at least more than some other criminals)
A six pack attack, Advanced Challenge (features the kanto and hoenn starters of the proffessors)
Seeing is believing, Advanced (Jessie has for a while believed her cascoon is a silcoon, and in this episode it and may's silcoon evolve)
Brave the Wave, Advanced (Ash's second hoenn gym battle, where Ash gets a little stubborn and presumptuous and it bites him in the but)
Having a Wailord of a Time, Advanced
I feel skitty, Advanced (May catches her skitty...and it's SOOO cute!)
Gaining Groudon/Stopping the Raging of Legends, Advanced Battle (The climax of the Team Magma/Aqua subplot in the anime)
The Princess and The Togepi/A togepi Mirage, Advanced Challenge (A two parter where Misty visits ash again and a new enemy is after her togepi...)
Gulpin it down!, Advanced Challenge (Involves candy that makes pokemon enormous sized, and it happens at parts to Jessie's Dustox, ash's treeko, and a wild gulpin)
Exploud and Clear!, Advanced Challenge (Ash's treeko evolves)
Take this House and Shuppet, Advanced Challenge (Ash's group and TR get stuck in an abondoned mansion with a shuppet that drains, and thus removes, feelings of anger from people)
A shroomish skirmish, Advanced Challenge (May's torchic evolves. Also has a small but very funny joke about how desperate Team Rocket is for food
)
Well that's Just Swellow!, Advanced Challenge (Ash's tailow, and Jessie's dustox under the command of James, compete in a aerial pokemon ringer competition)
There's a lot more ones I love, maybe I'll tell you more later, but check these out for now!