There was the C-One. It was primarily aimed at C64 enthusiasts but the Minimig and other cores were ported to it.
http://c64upgra.de/c-one/There was Natami. The original prototype used the C-One as it's basis with a custom 68030 card in a PCI slot.
http://translate.google.fr/translate?u=http://obligement.free.fr/articles/natami_nouvel_amiga_classic.php&sl=fr&tl=en&hl=fr&ie=UTF-8The NatamiLX board was later produced. I think there were 3 or so built for team members before the project fizzled out.
http://www.natami.net/hardware.htmWhile not an Amiga reimplementation, an offshoot of the Natami is the Phoenix Apollo 680x0 FPGA core accelerator project. The 68000 FPGA core Vampire 600 card gives simliar speed to an 68060.
http://www.apollo-core.com/Another project from Jens Schoenfeld was Clone-A. The was planned to be a cylce exact reimplementation of the Amiga. Jens made drop in FPGA replacements of the custom chips and took an A500 to a few shows and asked people to bring their own disks to try and find anything that didn't work on it.
The eventual intention was to have an ASIC fabbed but licensing issues with Amiga Inc forced him to shelve the project.
The Indivision scandoublers re-use some of the tech he developed during his research and it sounds as though some of the logic will be re-used on the Amiga Reloaded.
http://www.totalamiga.org/files/TA25_JensIviewExtract.pdf
