I can´t really decide..so here is a short list:
Best:
019-"I'm Gonna Get this Pachirisu...Is That OK!?
- I really liked Hikari in this one, Pachirisu was funny as well. The chemistry between pachi and Hikari was pretty sweet as well. The wonderful and wacky animation helped a lot as well.
020-"Pokemon Hunter J!"
- great suspense in this episode and , of course, J made this episode.
And, hey, it had Pokésho Poké***** No. 1 as well
051-"Tag Battle! The Finals!!"
- do I really need to say why? Croagunk stabbing a giant turtle, mukubird doing nothing, Honoka disappearing, Iwane, creepy guy, Buizel and a giant bug on a tag-team etc.
Worst:
024-"Confrontation! Satoshi vs. Pikachu!?"
-really boring, really unnecessary..."let´s **** up an old woman, because her Pokémon ran away!" isn´t an interesting story to me at all.
063-"The Urimoo Trio and the Steamy Battle!!"
The Onsen-scene at the end was nice, other than that...a kinda meh episode...
other episodes which were overall boring expect for 1-2 scenes for me are:
"Pachirisu is Inside Kabarudon's Mouth!?" ( seriously, Butch&Cassidy are in it, AND a Pokémon we saw a few episodes ago and yet it was a borefest. TR was just there to make jokes based on getting names wrong...the animation gave m eye-cancer)
"Poketch Acquisition Difficulty!?" ( The croagunk/Brock scene was nice, TR plan was a good one as well, other than that? Nothing.)
"Miru and Cayce and the Bottom of the Water!"
EDIT: I decided. Bold-text is your friend ^^