In 2012, Torlus wrote an open-source FPGA Atari Jaguar called JagNetLists. It was built for the Stratix-II FPGA in the Nios-II dev kit, and contained a working 68000 implementation. ElectronAsh has started the process of porting JagNetLists to MiSTer and just released his initial code on Github with the hope that someone can step in and help complete the work. The Jag core will benefit from the cycle-accurate Motorola 68000 soft-core by ijor.
Several people, including Ash, are working on PC Engine CD support for the TG16 core, and that same code will lay the foundation for Jaguar CD and Sega CD.
JagNetLists: https://github.com/Torlus/JagNetlists
MiSTer Jaguar Github: https://github.com/ElectronAsh/Jaguar_MiSTer_master
MiSTer Jaguar Atari Forums Thread: http://www.atari-forum.com/viewtopic.php?f=117&t=34810