My first entry isn't necessarily from geocities or the 90s but I needed to share it somewhere and maybe someone else shares my enthusiasm for the fringes of web design.
http://www.warnerbros.com/archive/spacejam/movie/jam.htm The official Space Jam website. A true relic!
Space Jam is apparently making a come back https://twitter.com/yrbff/status/575668375868817409
http://superbad.com. Technically it's art but it's from around that time.
A while ago, I created a subreddit for any that I find on my travels. Feel free to add any that you know of :)
zombo.com is and always will be my favorite thing on the internet.