Virtual Jaguar is a highly portable and a extremely capable Atari Jaguar emulator, it is regarded as one of the best Atari Jaguar emulators around and is currently the only Jaguar emulator that is in somewhat active development. The only other real emulator for the system appears to of ceased in development.
Virtual Jaguar is based on the source code that was released David Raingeard from his work on his own Jaguar Emulator, Potato Emulation. It also made use of Aaron Giles work on M.A.M.E. In particular it was the CoJag driver that was part of M.A.M.E, it also combined this with the Starscream 68000 emulator core. Over the years though the core has been replaced with several different iterations and has been rewritten by various developers. The current core is a heavily customized version of UAE’s 68000 core.
The Virtual Jaguar emulator manages to emulate all the major subsystems of the Atari Jaguar to varying degrees. So far they should be highly compatible, but like all things, it needs continuous work to eventually emulate the cores exactly and be able to successfully replicate the Atari Jaguar without any issues.