Chrono Compendium - Has an active community, fan projects, hacking guides, articles, features, scripts, guides, and more! It's the Wal-mart of Chrono Trigger sites! ^_~
Chrono Symphonic ReMix Project - A collection of symphonic remakes of the majority of Chrono Trigger's songs.
Brink of Time: The Chrono Trigger Fanlisting - As the title says, this is a Chrono Trigger fanlisting, and a rather popular one at that.
Chrono Trigger Novel Project - The people here are novelizing Chrono Trigger! Check it out! They also offer fan art, fan fics and various media.
IcyBrian's RPG Page - The ultimate site for RPG fan fics and fan art. Their Chrono Trigger section is vast.
Chrono Trigger Resurrection - This was a project to completely recreate Chrono Trigger in full 3D. From the screen shots and trailer provided, the quality of this remake is of very high quality, what you would expect a PS2 RPG to look like. Unfortunately, Square-Enix found out about it and demanded that they cease the project.
Chrono Trigger @ RPG Classics - RPG Classics' Chrono Trigger shrine. Think of it as a full walkthrough divided up into sections.
Chronicles | Legend of the Chrono Trigger - Dedicated to the Chrono Trigger series; providing a full walkthrough, some maps, scans, movie clips, fan fics, fan art, and more.
Chrono Continuum - A pretty site dedicated to the Chron Trigger series; providing info, media, downloads, and some other stuff.