in terms of defunct fansites, i have a whole page on my site dedicated to my favorites, but let me share a few stand-outs:
eevee's hq - an eevee-themed site from 2007. it was later moved to route 50, which is apparently still up today, but has a custom error displayed when you visit, so you can't access much. this is the website that inspired my own site name!
joey & jolty's home is a website i was quite frankly obsessed with as a puppy. the fact that it's still hosted and online is crazy! i remember telling the webmaster how much it meant to me within the last few years too. we both transitioned, it turns out, LOL!
tr's rockin is a no-brainer. people speak its named in awed whispers. haha. their [glitches list], glitchdex "truly bizarre glitch" list, mew trick page, fake pokemon list, fake games, and fake merch articles were all the rage back in the day! they later turned into more of a general con-and-cosplay business (their weapons prop guide was pretty cool!) haha, they even had a wii-compatible index for those using the wii to browse the internet! the article list is really extensive.
eonlight valley was a major inspiration to me when i was small, their noobs vs newbies rant is so legendary to me - i remember it regularly. i was extremely fixated on their eonquest mystery dungeon CYOA too - i still name my pmd partner pikachus "azula" to this day! this website is so full of stuff, i think anyone would have fun combing through it.
valley of nightmares was another one of my favorites.
and of course i'd be a fool not to mention lugia's island. i feel like some of its content mimics dragonfree's cave of dragonflies a bit, which is funny to me; i figure the culture of the community lended itself to that sort of habit. of course, i, being a tiny thing at the time, was just going 'TWO CAKES!!' the whole time, essentially.