Dixie X-Files
Website devoted to paranormal and cryptozoological phenomena occuring in the Southern United States. "Haints, Haunting, and Hoodoo" was its tagline. Articles on bizarre swamp gas, Deermen legends of the Everglades, and related things.
Gigan Species
Geocities fansite devoted entirely to Gigan fanart and fanfic. In this, the Gigans are an entire species of Kaiju. Site chronicles their adventures on their planet, and well as Godzilla's eventual defeat by a Gigan. (Update 06/30/2015: now at least part available at the more solid gigaleo.com)
Godzilla's Domain
Massive fansite that was around in 2001. Contained an extraordinary amount of Godzilla fanart, many CGI renderings. Also had a forum and an extensive fanfic section containing lengthy stories like "Godzilla vs. Pinky and the Brain" and "Godzilla on Gilligan's Island."
Procession of the Damned
Amazing site run by visual artist, writer, and pumpkin carver Steve Ring. Contained urban legends and related art, stories, horror art, a demonic bestiary, etc. It will be missed.
Alien Surgeon
Zakas's website. Contained music, music videos, visual art, and schizoid poetry and news clippings. Was interesting to say the least.
Los Angeles Grim Society
Lovable online presence of a morbid LA scene. Pleasant rendition of that funeral dirge played upon entry. Hosted Grimley's Believe It or Don't! comic, LA gravesites, and spooky LA legends.
The Castle Monster
Steve Ring's later site. Great ode to horror. RIP.
Kaiju HQ
Extensive Kaiju site. Kaiju stats and profiles, film reviews, fanfic, media, and a market.
Emoscene.com
Finally died in 2015. A classy social network. RIP.
Cryptozoology.com
Longstanding cryptozoology site. At its peak, it featured news, forums, a reliably active chatroom, tons of user-submitted pictures and stories. One favourite memory of mine was a joke piece of fan-art from around '01-'03 - it depicted the Chupacabra as a giant monster, preparing to ride the Space Needle to... either Mars or the Moon, and feed on the alien goats of those planets.
Stickam
The legendary Stickam - a site of endless cams and cam chatrooms.You could just start broadcasting and people would come and see.
Jignarania.com
2006-2025. I hoped I'd die first, but that didn't happen. It lasted 19 years, but things have lasted longer and still perished eventually.