Yahoo chat was a big one for me. Me and my friend would spend hours trying to chat with people. At one point we met a kid around our age and after talking online to him for a while tried to call him, but his mom answered the phone and was really mad and all three of us got in big trouble.
I remember the hours I would waste playing pop it on pogo.com (which apparently still exists). There use to be a lot of those free game websites, everyone kind of had their own and you'd trade favorites with your friends.
I vaguely remember an early 2000s humor website that I would check daily. I've been trying to think of the name for years, but it's eluded me. I do remember it hosted the widely popular flash about bombing Osama bin Laden set to the tune of the banana boat song.
Before Livejournal there was Blurty. Don't remember much of the community/mechanical side of Blurty, but I have lots of good personal memories from it.
A little latter on Newgrounds, Albino Blacksheep, YTMND, heck even 4chan and ED were fun times.
The most annoying thing about MySpace was that some people would have songs play once you went on their page at full fucking volume.
Probably one of the worst things I've ever done in my life was when I managed to rip the mp3 of 403 Forbiddena's Southern Cross from the 4chan City flash, put it on my profile and blog pages, and also hid the play button so you couldn't stop it. You either sat and got your face blasted off by terrible engrish and very loud guitars or you didn't get to read my thoughts on episode 8 of The Melancholy of Haruhi Suzumiya.