I recently acquired a few doujinshi by MIK Mikako (psuedonym). The majority of these are yaoi interpretations of Glenn and Magus, though some are comedic episodes with the full cast. MIK Mikako's print bibliography is here:
http://www.oldgaulcity.com/ogc/fanbooks/index.html, in both Japanese and English. Only one of the featured comics is not CT related. There are additionally two web comics here:
http://oldgaulcity.com/ogc/chrono/chrono-trigger.html. MIK Mikako can speak English though the majority of her site is in Japanese. I'm sure she would be happy to be included in the doujinshi database here.
I hope this is an appropriate place to suggest these new titles.