The episode I just mentioned, "Battle Aboard the St. Anne," was always one of my favorite Indigo-league episodes, and still is today. A good bulk of it is laugh-out-loud funny, has some great battle scenes, and ends with a neat Titanic-esque cliffhanger. For years, I've only known the English dub, as that's what I grew up on. However, for this post, I will be doing a more detailed comparison of the 4Kids English dub with the original Japanese version, even more detailed than the one on Dogasu's backpack...
In the original Japanese version, there is no background music from the title card up until Jessie and James appear in their "dopey teenage girl" disguises. 4Kids made sure the whole scene there had music, including calypso/steel drum music during Misty's fantasy of sunbathing on the deck.
In the English version, after Jessie says "Step this way!" James giggles in his cheesy falsetto voice. But in the original Japanese version, he's just saying "Cool!" again (the equivalent in Japanese is "Chou!") This was a sensible edit 4Kids did, I must admit, as it did look like James was giggling, plus it was an excuse to showcase more of Eric Stuart's talents on voicing James in drag (with that said, James had a somewhat more convincing feminine voice in the Japanese version, but the dub made him have the crummy falsetto voice we've known to love!)
When Jessie says "To - tal - ly... FREE!" in the Japanese version, she is saying "Pu - re - sen... TO!" (indicating they are a free present to our heroes.) This explains why in the dumb her mouth is making an "O" motion when saying "Free" (but I think that actually looks funny!)
Additionally, that whole scene from when Ash questions the buzz words Jessie is saying to Misty, up until Jessie drags James to that lighthouse, there is no background music in the Japanese version. 4Kids filled that gap with more nondescript stock music of their own.
The shot of James being hit after his "Don't I make the coolest girl" bit is animated differently in the Japanese version; we can briefly see a close-up of his reaction. He also doesn't say "Ow..." in his normal voice while being dragged away like he does in the dub.
Even though Persian doesn't say his name like he sometimes does, most of his vocal effects were re-dubbed in the 4Kids dub.
Again, no background music from Giovanni's chuckling until Ash and company enter that large room in the Japanese version. Not so in the dub.
When we see that barker saying "Come on, come all!" on the ship, they translated the Japanese writing on the sign next to him into English ("SALE!") To make it easier, rather than letting the film clip roll as usual, they just used a freeze-frame of the final frame of that shot and added a video zoom-out.
The three boys comparing their Charmanders and Squirtle have different voices in the Japanese version. The two boys with Charmanders have higher boy-like voices, while the boy with the Squirtle has a man's voice. In the dub, the first boy with the Charmander has a man-like voice, while the other two have higher voices.
After the Gentleman's Raticate beats that boy's Starmie, we get one of the better paint edits on the show. The Japanese "winner" sign has the kanji replaced with the English word "WIN," flashing in the same color and at the exact same tempo as the original. Even the pan-up to the sign looks good. The sound effect for the sign flashing was also changed in the 4Kids dub.
Additionally, no background music is heard in the original after Starmie's defeat, up until Ash begins battling the gentleman, but not so in the dub.
When Ash has fire in his eyes, in the Japanese version he's saying he's all fired up. The dub has him simply say "I can't wait!"
Butterfree doesn't really make any noise in that shot of Raticate and Butterfree repeatedly tackling each other in the air in the Japanese version. In the dub, he does (the probably just used old stock audio of Butterfree or something.)
The Japanese version has no music after the Gentleman picks up his paralyzed Raticate up until the Magikarp Salesman begins talking to James about Magikarp eggs and stuff, when the music cue used in the infamous cut "Beauty and the Beach" scene plays until James says "Chou!" (in the Japanese version) or "Rich! Rich!" (in the English dub.) 4Kids added all-new music to that scene, including replacing the existing music.
The artwork for Raticate in the Japanese "Who's That Pokemon" bit is different, showing him facing the camera. The dub just uses one of those typical late 1990s stock clip art images of Raticate instead. After that, rather than cut to the ship at sea, a fake fade was added in the dub.
More crashing wave noises were added as we see the St. Anne sailing along in the dub.
Again, more 4Kids background music was added to cover up silence from when the Gentleman talks to Ash about trading up to the actual trading process. They also replaced the music that plays in the original during the trade, and also added music to cover up silence during the scene when Jessie and Meowth are furious at James for buying the Magikarp.
Maybe this was censorship in Japan, but on the Japanese version I saw, we see two shots of cartoonish stars when James is hit. The 4Kids dub (at least on my DVD set) replaces that second star shot with blood and a tooth flying on a black background.
When we cut right to the St. Anne after that hilarious shot of Jessie beating up James, 4Kids added the sound of the ship's horn to that shot. We don't hear the horn in the Japanese version.
There was also no music during Ash and Misty's conversation following that in the Japanese version, but 4Kids covered that up...
Persain's Japanese "RAYAOOOOOO!!!" noise to signal the start of the Rocket attack was kept in the dub.
After Jessie announces that Team Rocket will take their Pokemon, in the Japanese version the crowd is silent. The 4Kids dub added a bunch of chatter from the crowd there (you can hear a Southern-sounding guy say "Our Pokah-mon?" and a boy saying "They can't do that!")
When the Geodudes all spinning around hit the Rocket grunts, this was slowed down in the dub. The Japanese version I watched had it moving at regular motion.
Ash's flashback of Metapod evolving into Butterfree and battling Staryu is accompanied by the "Maiden's Peak" music in the Japanese version (that soft, sad piano theme, in case you didn't know.) The dub replaces it with the music that was heard when Pikachu and Caterpie talked to each other in "Ash Catches a Pokemon."
(A side note: the sound effect used for Metapod evolving into Butterfree- the Japanese-sounding gong and choral effect- was also used in the dub of "Bye Bye Butterfree" during the appropriate flashback sequence, while the Japanese version had no sound effects for said flashbacks.)
Again, new music was added from when Jessie, James and Mewoth moan after defeat up to the crowd running for the lifeboats in the dub to cover up the lack of background music in the Japanese version.
(Heh, I think that "Run Away" music would probably accompany the actual Titanic evacuation/sinking very well...)
Ash doesn't say anything in the Japanese version when the force of the waves causes Butterfree's Pokeball to fly from his hands. In the dub, he shouts "NOOOO!!!"
4Kids added tense-sounding music when the Captain checks for missing people in a foolish manner. There was no music here in the Japanese version.
The original version had rather dark-sounding piano-based horror music accompanying the final scene. 4Kids added their own version for the dub, sounding a bit more like "stereotypical" horror music than real horror music.